6NB7

SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 2)

PDB DOI: https://doi.org/10.2210/pdb6NB7/pdb
EM Map EMD-0404: EMDB EMDataResource

Classification: VIRUS
Organism(s): Severe acute respiratory syndrome-related coronavirus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-12-06 Released: 2019-02-06
Deposition Author(s): Walls, A.C., Xiong, X., Park, Y.J., Tortorici, M.A., Snijder, S., Quispe, J., Cameroni, E., Gopal, R., Mian, D., Lanzavecchia, A., Zambon, M., Rey, F.A., Corti, D., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 526.24 kDa
Atom Count: 24,718
Modelled Residue Count: 3,828
Deposited Residue Count: 4,506
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,263	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594 Go to UniProtKB: P59594
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59594
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S230 heavy chain	D, F [auth G], G [auth H]	127	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S230 light chain	E, H [auth I], I [auth L]	112	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
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], CA [auth c], EA [auth e], HA [auth h], J [auth F], AA [auth a], CA [auth c], EA [auth e], HA [auth h], J [auth F], JA [auth j], K [auth J], L [auth K], LA [auth l], M, MA [auth m], N, NA [auth n], O, Q, RA [auth r], TA [auth t], V, X, Y, Z	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain J [auth F] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain Q Focus chain RA [auth r] Focus chain TA [auth t] Focus chain V Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain J [auth F] Focus chain JA [auth j] Focus chain K [auth J] Focus chain L [auth K] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain Q Focus chain RA [auth r] Focus chain TA [auth t] Focus chain V Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], P, QA [auth q], R, S, DA [auth d], P, QA [auth q], R, S, U	5		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain P Focus chain QA [auth q] Focus chain R Focus chain S Focus chain U Interactions & Density Focus chain DA [auth d] Focus chain P Focus chain QA [auth q] Focus chain R Focus chain S Focus chain U
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	SA [auth s], T	4		N-Glycosylation	Interactions Focus chain SA [auth s] Focus chain T Interactions & Density Focus chain SA [auth s] Focus chain T
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], IA [auth i], KA [auth k], OA [auth o], PA [auth p], BA [auth b], IA [auth i], KA [auth k], OA [auth o], PA [auth p], W	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain W Interactions & Density Focus chain BA [auth b] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain W
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], GA [auth g]	4		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain GA [auth g] Interactions & Density Focus chain FA [auth f] Focus chain GA [auth g]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth C], HB [auth C], IB [auth C], JB [auth C], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	RELION	3.0

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120553

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2019-02-20
Changes: Data collection, Database references, Other
Version 1.2: 2019-03-06
Changes: Data collection, Database references
Version 1.3: 2020-01-08
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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Help and Resources

6NB7

SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 2)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)