9F4B | pdb_00009f4b

Pre-assembled baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

PDB DOI: https://doi.org/10.2210/pdb9F4B/pdb
EM Map EMD-50187: EMDB EMDataResource

Classification: VIRUS
Organism(s): Klebsiella phage KP1
Mutation(s): No

Deposited: 2024-04-26 Released: 2025-05-14
Deposition Author(s): Orlova, E.V., Isupov, M.N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Orlova, E.V., Isupov, M.N.

To be published.

Macromolecule Content

Total Structure Weight: 6,577.15 kDa
Atom Count: 440,315
Modelled Residue Count: 56,329
Deposited Residue Count: 59,290
Unique protein chains: 16

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp6	A [auth AT] B [auth AV] C [auth AX] D [auth AS] E [auth AU] A [auth AT], B [auth AV], C [auth AX], D [auth AS], E [auth AU], F [auth AW], G [auth AN], H [auth AP], I [auth AR], J [auth AM], K [auth AO], L [auth AQ]	655	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5R4 (Klebsiella phage KP1) Explore A0A2K9V5R4 Go to UniProtKB: A0A2K9V5R4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5R4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate tail tube cap	M [auth BL] N [auth BN] O [auth BP] P [auth BK] Q [auth BM] M [auth BL], N [auth BN], O [auth BP], P [auth BK], Q [auth BM], R [auth BO]	350	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V618 (Klebsiella phage KP1) Explore A0A2K9V618 Go to UniProtKB: A0A2K9V618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V618
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate subunit	S [auth BQ] T [auth BR] U [auth BS] V [auth BT] W [auth BU] S [auth BQ], T [auth BR], U [auth BS], V [auth BT], W [auth BU], X [auth BV]	308	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A7I8V4E3 (Klebsiella phage vB_KpnM_311F) Explore A0A7I8V4E3 Go to UniProtKB: A0A7I8V4E3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7I8V4E3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit	AA [auth AL] BA [auth AG] CA [auth AI] DA [auth AK] Y [auth AH] AA [auth AL], BA [auth AG], CA [auth AI], DA [auth AK], Y [auth AH], Z [auth AJ]	212	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5R5 (Klebsiella phage KP1) Explore A0A2K9V5R5 Go to UniProtKB: A0A2K9V5R5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5R5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate central spike protein	EA [auth BB], FA [auth BC], GA [auth BD]	576	Klebsiella phage KP1	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for A0A976LXP5 (Klebsiella phage vB_KpnM_5N) Explore A0A976LXP5 Go to UniProtKB: A0A976LXP5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A976LXP5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase	HA [auth BA]	97	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5W6 (Klebsiella phage KP1) Explore A0A2K9V5W6 Go to UniProtKB: A0A2K9V5W6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5W6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp7	IA [auth AY] JA [auth A2] KA [auth AZ] LA [auth A0] MA [auth A1] IA [auth AY], JA [auth A2], KA [auth AZ], LA [auth A0], MA [auth A1], NA [auth A3]	1,032	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5T9 (Klebsiella phage KP1) Explore A0A2K9V5T9 Go to UniProtKB: A0A2K9V5T9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5T9
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit	OA [auth Ad] PA [auth Ac] QA [auth Ab] RA [auth Aa] SA [auth Ae] OA [auth Ad], PA [auth Ac], QA [auth Ab], RA [auth Aa], SA [auth Ae], TA [auth Af], UA [auth A4], VA [auth A5], WA [auth A6], XA [auth A7], YA [auth A8], ZA [auth A9]	341	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2Z4QAY9 (Klebsiella phage Mineola) Explore A0A2Z4QAY9 Go to UniProtKB: A0A2Z4QAY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2Z4QAY9
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge tail fiber connector	AB [auth LA] BB [auth LB] CB [auth LC] DB [auth LD] EB [auth LE] AB [auth LA], BB [auth LB], CB [auth LC], DB [auth LD], EB [auth LE], FB [auth LF], GB [auth LG], HB [auth LH], IB [auth LI], JB [auth LJ], KB [auth LK], LB [auth LL], MB [auth LM], NB [auth LN], OB [auth LO], PB [auth LP], QB [auth LQ], RB [auth LR]	303	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5S1 (Klebsiella phage KP1) Explore A0A2K9V5S1 Go to UniProtKB: A0A2K9V5S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5S1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp10	AC [auth FU] BC [auth Fb] CC [auth Fc] DC [auth Fd] EC [auth Fk] AC [auth FU], BC [auth Fb], CC [auth Fc], DC [auth Fd], EC [auth Fk], FC [auth Fl], GC [auth Fm], HC [auth Ft], IC [auth Fu], JC [auth Fv], SB [auth FA], TB [auth FB], UB [auth FC], VB [auth FJ], WB [auth FK], XB [auth FL], YB [auth FS], ZB [auth FT]	607	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5S8 (Klebsiella phage KP1) Explore A0A2K9V5S8 Go to UniProtKB: A0A2K9V5S8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5S8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge subunit and tail pin	AD [auth Fx] BD [auth Fy] KC [auth FD] LC [auth FE] MC [auth FF] AD [auth Fx], BD [auth Fy], KC [auth FD], LC [auth FE], MC [auth FF], NC [auth FM], OC [auth FN], PC [auth FO], QC [auth FV], RC [auth FW], SC [auth FX], TC [auth Fe], UC [auth Ff], VC [auth Fg], WC [auth Fn], XC [auth Fo], YC [auth Fp], ZC [auth Fw]	223	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5T5 (Klebsiella phage KP1) Explore A0A2K9V5T5 Go to UniProtKB: A0A2K9V5T5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5T5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Gp12 short tail fibers	CD [auth FG] DD [auth FI] ED [auth FH] FD [auth FP] GD [auth FR] CD [auth FG], DD [auth FI], ED [auth FH], FD [auth FP], GD [auth FR], HD [auth FQ], ID [auth FY], JD [auth Fa], KD [auth FZ], LD [auth Fh], MD [auth Fj], ND [auth Fi], OD [auth Fq], PD [auth Fs], QD [auth Fr], RD [auth Fz], SD [auth F2], TD [auth F1]	448	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A7R8MRX7 (Klebsiella phage vB_KpM-Wobble) Explore A0A7R8MRX7 Go to UniProtKB: A0A7R8MRX7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R8MRX7
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein	AE [auth B3] BE [auth B4] CE [auth B5] DE [auth B6] EE [auth B7] AE [auth B3], BE [auth B4], CE [auth B5], DE [auth B6], EE [auth B7], FE [auth B8], UD [auth BW], VD [auth BX], WD [auth BY], XD [auth BZ], YD [auth B1], ZD [auth B2]	163	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5T6 (Klebsiella phage KP1) Explore A0A2K9V5T6 Go to UniProtKB: A0A2K9V5T6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5T6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
IraD/Gp25-like domain-containing protein	GE [auth AA] HE [auth AB] IE [auth AC] JE [auth AD] KE [auth AE] GE [auth AA], HE [auth AB], IE [auth AC], JE [auth AD], KE [auth AE], LE [auth AF]	136	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A0K1Y5J2 (Klebsiella phage JD18) Explore A0A0K1Y5J2 Go to UniProtKB: A0A0K1Y5J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K1Y5J2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative baseplate hub subunit	ME [auth BE], NE [auth BF], OE [auth BG]	380	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A7T3TJP2 (Klebsiella phage vB_KpnM_BovinicusUrsus) Explore A0A7T3TJP2 Go to UniProtKB: A0A7T3TJP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7T3TJP2
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate hub subunit tail length determinator	PE [auth BH], QE [auth BI], RE [auth BJ]	577	Klebsiella phage KP1	Mutation(s): 0
UniProt
Find proteins for A0A2K9V5Z4 (Klebsiella phage KP1) Explore A0A2K9V5Z4 Go to UniProtKB: A0A2K9V5Z4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K9V5Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AF [auth Fc] SDF format, chain CF [auth Fl] SDF format, chain EF [auth FG] SDF format, chain UE [auth FB] SDF format, chain WE [auth FK] SDF format, chain YE [auth FT] MOL2 format, chain AF [auth Fc] MOL2 format, chain CF [auth Fl] MOL2 format, chain EF [auth FG] MOL2 format, chain UE [auth FB] MOL2 format, chain WE [auth FK] MOL2 format, chain YE [auth FT] mmCIF format, chain AF [auth Fc] mmCIF format, chain CF [auth Fl] mmCIF format, chain EF [auth FG] mmCIF format, chain UE [auth FB] mmCIF format, chain WE [auth FK] mmCIF format, chain YE [auth FT]	AF [auth Fc] CF [auth Fl] EF [auth FG] UE [auth FB] WE [auth FK] AF [auth Fc], CF [auth Fl], EF [auth FG], UE [auth FB], WE [auth FK], YE [auth FT]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AF [auth Fc] Focus chain CF [auth Fl] Focus chain EF [auth FG] Focus chain UE [auth FB] Focus chain WE [auth FK] Focus chain YE [auth FT] Interactions & Density Focus chain AF [auth Fc] Focus chain CF [auth Fl] Focus chain EF [auth FG] Focus chain UE [auth FB] Focus chain WE [auth FK] Focus chain YE [auth FT]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain BF [auth Fk] SDF format, chain DF [auth Ft] SDF format, chain TE [auth FA] SDF format, chain VE [auth FJ] SDF format, chain XE [auth FS] SDF format, chain ZE [auth Fb] MOL2 format, chain BF [auth Fk] MOL2 format, chain DF [auth Ft] MOL2 format, chain TE [auth FA] MOL2 format, chain VE [auth FJ] MOL2 format, chain XE [auth FS] MOL2 format, chain ZE [auth Fb] mmCIF format, chain BF [auth Fk] mmCIF format, chain DF [auth Ft] mmCIF format, chain TE [auth FA] mmCIF format, chain VE [auth FJ] mmCIF format, chain XE [auth FS] mmCIF format, chain ZE [auth Fb]	BF [auth Fk] DF [auth Ft] TE [auth FA] VE [auth FJ] XE [auth FS] BF [auth Fk], DF [auth Ft], TE [auth FA], VE [auth FJ], XE [auth FS], ZE [auth Fb]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BF [auth Fk] Focus chain DF [auth Ft] Focus chain TE [auth FA] Focus chain VE [auth FJ] Focus chain XE [auth FS] Focus chain ZE [auth Fb] Interactions & Density Focus chain BF [auth Fk] Focus chain DF [auth Ft] Focus chain TE [auth FA] Focus chain VE [auth FJ] Focus chain XE [auth FS] Focus chain ZE [auth Fb]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain SE [auth BB] MOL2 format, chain SE [auth BB] mmCIF format, chain SE [auth BB]	SE [auth BB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain SE [auth BB] Interactions & Density Focus chain SE [auth BB]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3
MODEL REFINEMENT	REFMAC
MODEL REFINEMENT	ISOLDE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Orlova, E.V.

Isupov, M.N.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9F4B | pdb_00009f4b

Pre-assembled baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Sequence Annotations

Entity ID: 7

UniProt

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Sequence Annotations

Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

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Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

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Sequence Annotations

Entity ID: 16

UniProt

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9F4B | pdb_00009f4b