8YUC | pdb_00008yuc

Crystal structure of SARS-CoV-2 ConSp RBD in complex with antibodies PDI222 Fab and COVA1-16 Fab

PDB DOI: https://doi.org/10.2210/pdb8YUC/pdb

Classification: IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Spodoptera frugiperda, Homo sapiens
Mutation(s): Yes

Deposited: 2024-03-27 Released: 2025-10-01
Deposition Author(s): Kang, J.M., Yuan, M., Han, B.W., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation, National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.51 Å
R-Value Free:
0.308 (Depositor), 0.305 (DCC)
R-Value Work:
0.275 (Depositor), 0.275 (DCC)
R-Value Observed:
0.276 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and antigenic characteristics of consensus sequence-based SARS-CoV-2 antigen

Kang, J.M., Yuan, M., Han, B.W., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 117.95 kDa
Atom Count: 8,167
Modeled Residue Count: 1,065
Deposited Residue Count: 1,079
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	A [auth G]	196	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 24 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
PDI222 heavy chain	B [auth A]	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PDI222 light chain	C [auth B]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COVA1-16 heavy chain	D [auth H]	231	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COVA1-16 light chain	E [auth L]	213	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.51 Å
R-Value Free: 0.308 (Depositor), 0.305 (DCC)
R-Value Work: 0.275 (Depositor), 0.275 (DCC)
R-Value Observed: 0.276 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.264	α = 90
b = 127.264	β = 90
c = 240.894	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019R1A2C1090251
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2023-00218543