7UPW

Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment

PDB DOI: https://doi.org/10.2210/pdb7UPW/pdb
EM Map EMD-26676: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus, Homo sapiens, Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-04-18 Released: 2022-08-10
Deposition Author(s): Zhang, J., Luo, S., Kreutzberger, A., Kirchhausen, T., Chen, B., Haynes, B., Alt, F.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Massachusetts Consortium on Pathogen Readiness (MassCPR), Mercatus Center

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 678.15 kDa
Atom Count: 37,893
Modelled Residue Count: 4,674
Deposited Residue Count: 5,922
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	1,310	Severe acute respiratory syndrome coronavirus	Mutation(s): 1 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SP1-77 Fab heavy chain	D, F, H	451	Homo sapiens, Mus musculus	Mutation(s): 0
Entity Groups
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Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SP1-77 Fab light chain	E, G, I [auth L]	213	Homo sapiens, Mus musculus	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], J [auth I], LA [auth l], N, V, HA [auth h], J [auth I], LA [auth l], N, V, Z	2		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain J [auth I] Focus chain LA [auth l] Focus chain N Focus chain V Focus chain Z Interactions & Density Focus chain HA [auth h] Focus chain J [auth I] Focus chain LA [auth l] Focus chain N Focus chain V Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], DA [auth d], EA [auth e], GA [auth g], AA [auth a], BA [auth b], DA [auth d], EA [auth e], GA [auth g], IA [auth i], JA [auth j], K [auth J], KA [auth k], L [auth K], M, MA [auth m], NA [auth n], O, P, PA [auth p], QA [auth q], R, S, SA [auth s], U, W, X, Y	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain U Focus chain W Focus chain X Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth J] Focus chain KA [auth k] Focus chain L [auth K] Focus chain M Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain U Focus chain W Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], FA [auth f], OA [auth o], Q, RA [auth r], CA [auth c], FA [auth f], OA [auth o], Q, RA [auth r], T	3		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain FA [auth f] Focus chain OA [auth o] Focus chain Q Focus chain RA [auth r] Focus chain T Interactions & Density Focus chain CA [auth c] Focus chain FA [auth f] Focus chain OA [auth o] Focus chain Q Focus chain RA [auth r] Focus chain T
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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 LB [auth C] 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 B] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain TA [auth A] 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 LB [auth C] 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 B] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain TA [auth A] 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 B], HB [auth C], IB [auth C], JB [auth C], KB [auth C], LB [auth C], MB [auth C], NB [auth C], TA [auth A], 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 B] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain TA [auth A] 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 B] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain TA [auth A] 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: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	INV-021989
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI27193
Massachusetts Consortium on Pathogen Readiness (MassCPR)	United States	SARS-CoV-2 Variants Award
Mercatus Center	United States	Emergent Ventures Fast Grant