7Y0O | pdb_00007y0o

Interface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody

PDB DOI: https://doi.org/10.2210/pdb7Y0O/pdb
EM Map EMD-33551: EMDB EMDataResource

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

Deposited: 2022-06-05 Released: 2023-09-06
Deposition Author(s): Wang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7Y0O

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

Literature

SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody

Wang, L.

To be published.

Macromolecule Content

Total Structure Weight: 59.55 kDa
Atom Count: 4,185
Modeled Residue Count: 541
Deposited Residue Count: 541
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	194	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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of R15	B [auth H]	116	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of R15	C [auth L]	108	Homo sapiens	Mutation(s): 0

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
P14 nanobody	D [auth B]	123	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-09-06
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary
Version 1.2: 2025-07-02
Changes: Data collection

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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.