8GDR

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10

PDB DOI: https://doi.org/10.2210/pdb8GDR/pdb
EM Map EMD-29950: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-03-06 Released: 2024-03-13
Deposition Author(s): Patel, A., Ortlund, E.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody

Patel, A., Kumar, S., Lai, L., Chakravarthy, C., Valanparambil, R., Keen, M., Laughlin, Z.T., Frank, F., Cheedarla, N., Verkerke, H.P., Neish, A.S., Roback, J.D., Davis, C.W., Wrammert, J., Ahmed, R., Suthar, M.S., Murali-Krishna, K., Chandele, A., Ortlund, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 488.14 kDa
Atom Count: 32,331
Modelled Residue Count: 4,104
Deposited Residue Count: 4,384
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, D [auth E], E [auth F]	1,168	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain D [auth E] Focus chain E [auth F]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 002-S21B10 heavy chain variable domain	B [auth C], F [auth H]	224	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 002-S21B10 light chain variable domain	C [auth D], G [auth J]	216	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth c], I [auth e], J [auth g], K [auth i]	2		N-Glycosylation	Interactions Focus chain H [auth c] Focus chain I [auth e] Focus chain J [auth g] Focus chain K [auth i] Interactions & Density Focus chain H [auth c] Focus chain I [auth e] Focus chain J [auth g] Focus chain K [auth i]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain LA [auth F] SDF format, chain MA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain FA [auth F] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain X [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain X [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain X [auth E]	AA [auth E] BA [auth E] CA [auth F] DA [auth F] EA [auth F] AA [auth E], BA [auth E], CA [auth F], DA [auth F], EA [auth F], FA [auth F], GA [auth F], HA [auth F], IA [auth F], JA [auth F], KA [auth F], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth E], W [auth E], X [auth E], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Patel, A.

Ortlund, E.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5U19 AI14237-04 (subaward 000520244-SP008-SC014)