9DN4

Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N

PDB DOI: https://doi.org/10.2210/pdb9DN4/pdb
NAKB: 9DN4

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Severe acute respiratory syndrome coronavirus 2
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-09-16 Released: 2024-09-25
Deposition Author(s): Lovell, S., Cooper, A., Battaile, K.P., Hegde, S., Wang, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.176
R-Value Observed: 0.178

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N

Lovell, S., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 118.26 kDa
Atom Count: 8,028
Modelled Residue Count: 896
Deposited Residue Count: 1,006
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB BL3-6S97N HEAVY CHAIN	A, D	250	Mus musculus	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB BL3-6S97N LIGHT CHAIN	B, C	233	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PCPUPCPGPUPCPUPGPAPAPAPCPAPCPGPGPAPGPAPG)-3')	E, F	20	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E]	I [auth A] L [auth B] M [auth B] R [auth C] S [auth C] I [auth A], L [auth B], M [auth B], R [auth C], S [auth C], W [auth D], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth D] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain U [auth D]	G [auth A], J [auth B], N [auth C], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain U [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E]	H [auth A] K [auth B] O [auth C] P [auth C] Q [auth C] H [auth A], K [auth B], O [auth C], P [auth C], Q [auth C], V [auth D], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.726	α = 90
b = 68.025	β = 100.16
c = 118.615	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM147498
National Institutes of Health/Office of the Director	United States	S10OD030394