8TRZ | pdb_00008trz

Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin

PDB DOI: https://doi.org/10.2210/pdb8TRZ/pdb
EM Map EMD-41586: EMDB EMDataResource

Classification: OXYGEN TRANSPORT
Organism(s): Pomacea canaliculata
Mutation(s): No

Deposited: 2023-08-10 Released: 2025-04-02
Deposition Author(s): Brola, T.R., Chiumiento, I.R., Gragera, M., Carazo, J.M., Heras, H., Dreon, M.S., Otero, L.H.
Funding Organization(s): Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin

Brola, T.R., Chiumiento, I.R., Gragera, M., Carazo, J.M., Heras, H., Dreon, M.S., Otero, L.H.

To be published.

Macromolecule Content

Total Structure Weight: 7,831.14 kDa
Atom Count: 549,912
Modelled Residue Count: 67,750
Deposited Residue Count: 68,160
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemocyanin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	3,408	Pomacea canaliculata	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], AD [auth qA], BC [auth RA], CB [auth 2], CC [auth SA], AB [auth 0], AD [auth qA], BC [auth RA], CB [auth 2], CC [auth SA], DA [auth d], EA [auth e], EC [auth UA], FD [auth vA], GA [auth g], GC [auth WA], GD [auth wA], HB [auth 7], IA [auth i], IB [auth 8], ID [auth yA], KB [auth AA], KD [auth 0A], LC [auth bA], MB [auth CA], MC [auth cA], NA [auth n], OA [auth o], OC [auth eA], PD [auth 5A], QA [auth q], QC [auth gA], RB [auth HA], SA [auth s], SB [auth IA], U, UB [auth KA], VC [auth lA], W, WB [auth MA], WC [auth mA], XA [auth x], Y, YA [auth y], YC [auth oA]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain AD [auth qA] Focus chain BC [auth RA] Focus chain CB [auth 2] Focus chain CC [auth SA] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EC [auth UA] Focus chain FD [auth vA] Focus chain GA [auth g] Focus chain GC [auth WA] Focus chain GD [auth wA] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain ID [auth yA] Focus chain KB [auth AA] Focus chain KD [auth 0A] Focus chain LC [auth bA] Focus chain MB [auth CA] Focus chain MC [auth cA] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain OC [auth eA] Focus chain PD [auth 5A] Focus chain QA [auth q] Focus chain QC [auth gA] Focus chain RB [auth HA] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain U Focus chain UB [auth KA] Focus chain VC [auth lA] Focus chain W Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain YC [auth oA] Interactions & Density Focus chain AB [auth 0] Focus chain AD [auth qA] Focus chain BC [auth RA] Focus chain CB [auth 2] Focus chain CC [auth SA] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EC [auth UA] Focus chain FD [auth vA] Focus chain GA [auth g] Focus chain GC [auth WA] Focus chain GD [auth wA] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain ID [auth yA] Focus chain KB [auth AA] Focus chain KD [auth 0A] Focus chain LC [auth bA] Focus chain MB [auth CA] Focus chain MC [auth cA] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain OC [auth eA] Focus chain PD [auth 5A] Focus chain QA [auth q] Focus chain QC [auth gA] Focus chain RB [auth HA] Focus chain SA [auth s] Focus chain SB [auth IA] Focus chain U Focus chain UB [auth KA] Focus chain VC [auth lA] Focus chain W Focus chain WB [auth MA] Focus chain WC [auth mA] Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain YC [auth oA]

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], AC [auth QA], BA [auth b], BB [auth 1], BD [auth rA], AA [auth a], AC [auth QA], BA [auth b], BB [auth 1], BD [auth rA], CA [auth c], CD [auth sA], DB [auth 3], DC [auth TA], DD [auth tA], EB [auth 4], ED [auth uA], FA [auth f], FB [auth 5], FC [auth VA], GB [auth 6], HA [auth h], HC [auth XA], HD [auth xA], IC [auth YA], JA [auth j], JB [auth 9], JC [auth ZA], JD [auth zA], KA [auth k], KC [auth aA], LA [auth l], LB [auth BA], LD [auth 1A], MA [auth m], MD [auth 2A], NB [auth DA], NC [auth dA], ND [auth 3A], OB [auth EA], OD [auth 4A], PA [auth p], PB [auth FA], PC [auth fA], QB [auth GA], RA [auth r], RC [auth hA], SC [auth iA], TA [auth t], TB [auth JA], TC [auth jA], UA [auth u], UC [auth kA], V, VA [auth v], VB [auth LA], WA [auth w], X, XB [auth NA], XC [auth nA], YB [auth OA], Z, ZA [auth z], ZB [auth PA], ZC [auth pA]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AC [auth QA] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain BD [auth rA] Focus chain CA [auth c] Focus chain CD [auth sA] Focus chain DB [auth 3] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain EB [auth 4] Focus chain ED [auth uA] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HC [auth XA] Focus chain HD [auth xA] Focus chain IC [auth YA] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain JD [auth zA] Focus chain KA [auth k] Focus chain KC [auth aA] Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain LD [auth 1A] Focus chain MA [auth m] Focus chain MD [auth 2A] Focus chain NB [auth DA] Focus chain NC [auth dA] Focus chain ND [auth 3A] Focus chain OB [auth EA] Focus chain OD [auth 4A] Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain QB [auth GA] Focus chain RA [auth r] Focus chain RC [auth hA] Focus chain SC [auth iA] Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain TC [auth jA] Focus chain UA [auth u] Focus chain UC [auth kA] Focus chain V Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain WA [auth w] Focus chain X Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain YB [auth OA] Focus chain Z Focus chain ZA [auth z] Focus chain ZB [auth PA] Focus chain ZC [auth pA] Interactions & Density Focus chain AA [auth a] Focus chain AC [auth QA] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain BD [auth rA] Focus chain CA [auth c] Focus chain CD [auth sA] Focus chain DB [auth 3] Focus chain DC [auth TA] Focus chain DD [auth tA] Focus chain EB [auth 4] Focus chain ED [auth uA] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain FC [auth VA] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HC [auth XA] Focus chain HD [auth xA] Focus chain IC [auth YA] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain JC [auth ZA] Focus chain JD [auth zA] Focus chain KA [auth k] Focus chain KC [auth aA] Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain LD [auth 1A] Focus chain MA [auth m] Focus chain MD [auth 2A] Focus chain NB [auth DA] Focus chain NC [auth dA] Focus chain ND [auth 3A] Focus chain OB [auth EA] Focus chain OD [auth 4A] Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain PC [auth fA] Focus chain QB [auth GA] Focus chain RA [auth r] Focus chain RC [auth hA] Focus chain SC [auth iA] Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain TC [auth jA] Focus chain UA [auth u] Focus chain UC [auth kA] Focus chain V Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain WA [auth w] Focus chain X Focus chain XB [auth NA] Focus chain XC [auth nA] Focus chain YB [auth OA] Focus chain Z Focus chain ZA [auth z] Focus chain ZB [auth PA] Focus chain ZC [auth pA]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AE [auth K] SDF format, chain BE [auth L] SDF format, chain CE [auth M] SDF format, chain DE [auth N] SDF format, chain EE [auth O] SDF format, chain FE [auth P] SDF format, chain GE [auth Q] SDF format, chain HE [auth R] SDF format, chain IE [auth S] SDF format, chain JE [auth T] SDF format, chain QD [auth A] SDF format, chain RD [auth B] SDF format, chain SD [auth C] SDF format, chain TD [auth D] SDF format, chain UD [auth E] SDF format, chain VD [auth F] SDF format, chain WD [auth G] SDF format, chain XD [auth H] SDF format, chain YD [auth I] SDF format, chain ZD [auth J] MOL2 format, chain AE [auth K] MOL2 format, chain BE [auth L] MOL2 format, chain CE [auth M] MOL2 format, chain DE [auth N] MOL2 format, chain EE [auth O] MOL2 format, chain FE [auth P] MOL2 format, chain GE [auth Q] MOL2 format, chain HE [auth R] MOL2 format, chain IE [auth S] MOL2 format, chain JE [auth T] MOL2 format, chain QD [auth A] MOL2 format, chain RD [auth B] MOL2 format, chain SD [auth C] MOL2 format, chain TD [auth D] MOL2 format, chain UD [auth E] MOL2 format, chain VD [auth F] MOL2 format, chain WD [auth G] MOL2 format, chain XD [auth H] MOL2 format, chain YD [auth I] MOL2 format, chain ZD [auth J] mmCIF format, chain AE [auth K] mmCIF format, chain BE [auth L] mmCIF format, chain CE [auth M] mmCIF format, chain DE [auth N] mmCIF format, chain EE [auth O] mmCIF format, chain FE [auth P] mmCIF format, chain GE [auth Q] mmCIF format, chain HE [auth R] mmCIF format, chain IE [auth S] mmCIF format, chain JE [auth T] mmCIF format, chain QD [auth A] mmCIF format, chain RD [auth B] mmCIF format, chain SD [auth C] mmCIF format, chain TD [auth D] mmCIF format, chain UD [auth E] mmCIF format, chain VD [auth F] mmCIF format, chain WD [auth G] mmCIF format, chain XD [auth H] mmCIF format, chain YD [auth I] mmCIF format, chain ZD [auth J]	AE [auth K] BE [auth L] CE [auth M] DE [auth N] EE [auth O] AE [auth K], BE [auth L], CE [auth M], DE [auth N], EE [auth O], FE [auth P], GE [auth Q], HE [auth R], IE [auth S], JE [auth T], QD [auth A], RD [auth B], SD [auth C], TD [auth D], UD [auth E], VD [auth F], WD [auth G], XD [auth H], YD [auth I], ZD [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AE [auth K] Focus chain BE [auth L] Focus chain CE [auth M] Focus chain DE [auth N] Focus chain EE [auth O] Focus chain FE [auth P] Focus chain GE [auth Q] Focus chain HE [auth R] Focus chain IE [auth S] Focus chain JE [auth T] Focus chain QD [auth A] Focus chain RD [auth B] Focus chain SD [auth C] Focus chain TD [auth D] Focus chain UD [auth E] Focus chain VD [auth F] Focus chain WD [auth G] Focus chain XD [auth H] Focus chain YD [auth I] Focus chain ZD [auth J] Interactions & Density Focus chain AE [auth K] Focus chain BE [auth L] Focus chain CE [auth M] Focus chain DE [auth N] Focus chain EE [auth O] Focus chain FE [auth P] Focus chain GE [auth Q] Focus chain HE [auth R] Focus chain IE [auth S] Focus chain JE [auth T] Focus chain QD [auth A] Focus chain RD [auth B] Focus chain SD [auth C] Focus chain TD [auth D] Focus chain UD [auth E] Focus chain VD [auth F] Focus chain WD [auth G] Focus chain XD [auth H] Focus chain YD [auth I] Focus chain ZD [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	Scipion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2021-00158
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2020- SERIEA-03047