7FAT | pdb_00007fat

Structure Determination of the RBD-NB1A7

PDB DOI: https://doi.org/10.2210/pdb7FAT/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus bactrianus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-07 Released: 2022-05-18
Deposition Author(s): Geng, Y., Shi, Z.Z., Li, X.Y., Wang, L., Sun, Z.C., Zhang, H.W., Chen, X.C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.193 (Depositor), 0.191 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Shi, Z., Li, X., Wang, L., Sun, Z., Zhang, H., Chen, X., Cui, Q., Qiao, H., Lan, Z., Zhang, X., Li, X., Li, L., Xu, J., Gong, R., Fan, C., Geng, Y.

(2022) Structure 30: 707

DOI: https://doi.org/10.1016/j.str.2022.02.011

Macromolecule Content

Total Structure Weight: 39.85 kDa
Atom Count: 2,711
Modeled Residue Count: 316
Deposited Residue Count: 357
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	219	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nb_1A7	B	138	Camelus bactrianus	Mutation(s): 0

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.193 (Depositor), 0.191 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.663	α = 90
b = 183.795	β = 90
c = 42.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31670743

Revision History (Full details and data files)

Version 1.0: 2022-05-18
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.