7EAM

immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6

PDB DOI: https://doi.org/10.2210/pdb7EAM/pdb

Classification: VIRAL PROTEIN, IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2021-03-07 Released: 2021-03-17
Deposition Author(s): Li, T.T., Gu, Y., Li, S.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.174
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants.

Li, T., Xue, W., Zheng, Q., Song, S., Yang, C., Xiong, H., Zhang, S., Hong, M., Zhang, Y., Yu, H., Zhang, Y., Sun, H., Huang, Y., Deng, T., Chi, X., Li, J., Wang, S., Zhou, L., Chen, T., Wang, Y., Cheng, T., Zhang, T., Yuan, Q., Zhao, Q., Zhang, J., McLellan, J.S., Zhou, Z.H., Zhang, Z., Li, S., Gu, Y., Xia, N.

(2021) Nat Commun 12: 5652

DOI: https://doi.org/10.1038/s41467-021-25997-3

Macromolecule Content

Total Structure Weight: 149.02 kDa
Atom Count: 11,106
Modelled Residue Count: 1,266
Deposited Residue Count: 1,334
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 protein S1	A, D [auth B]	233	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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
the heavy chain of Fab fragment of antibody 7D6	B [auth H], E [auth C]	220	Mus musculus	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
the light chain of Fab fragment of antibody 7D6	C [auth L], F [auth D]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	G [auth E], H [auth F]	2		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain G [auth E] Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 I [auth A] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B]	I [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.174
R-Value Observed: 0.174
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.44	α = 89.96
b = 87.97	β = 87.05
c = 102.72	γ = 89.98

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Li, T.T.

Gu, Y.

Li, S.W.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82001756

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2021-03-31
Changes: Derived calculations
Version 2.0: 2021-10-20
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
Version 3.0: 2021-11-10
Changes: Atomic model, Data collection, Derived calculations
Version 3.1: 2023-11-29
Changes: Data collection, Refinement description