8X7F | pdb_00008x7f

CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb8X7F/pdb
EM Map EMD-38098: EMDB EMDataResource

Classification: CELL INVASION
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-11-24 Released: 2024-12-04
Deposition Author(s): Jiang, W.X., Dong, X., Cheng, X.Q., Ma, L.X., Xing, Q.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8X7F

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

Literature

CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD

Jiang, W.X., Dong, X., Cheng, X.Q., Ma, L.X., Xing, Q.

To be published.

Macromolecule Content

Total Structure Weight: 164.61 kDa
Atom Count: 11,596
Modeled Residue Count: 1,388
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trifunctional NAD biosynthesis/regulator protein NadR	A, B [auth D], C [auth G], D [auth J]	347	Escherichia coli K-12	Mutation(s): 0 Gene Names: nadR, nadI, b4390, JW5800 EC: 2.7.7.1 (PDB Primary Data), 2.7.1.22 (PDB Primary Data)
UniProt
Find proteins for P27278 (Escherichia coli (strain K12)) Explore P27278 Go to UniProtKB: P27278
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27278
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth D] SDF format, chain I [auth G] SDF format, chain K [auth J] MOL2 format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain I [auth G] MOL2 format, chain K [auth J] mmCIF format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain I [auth G] mmCIF format, chain K [auth J]	E [auth A], G [auth D], I [auth G], K [auth J]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Focus chain I [auth G] Focus chain K [auth J] Interactions & Density Focus chain E [auth A] Focus chain G [auth D] Focus chain I [auth G] Focus chain K [auth J]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] SDF format, chain J [auth G] SDF format, chain L [auth J] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain J [auth G] MOL2 format, chain L [auth J] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain J [auth G] mmCIF format, chain L [auth J]	F [auth A], H [auth D], J [auth G], L [auth J]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain H [auth D] Focus chain J [auth G] Focus chain L [auth J] Interactions & Density Focus chain F [auth A] Focus chain H [auth D] Focus chain J [auth G] Focus chain L [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2021YFC2100100

Revision History (Full details and data files)

Version 1.0: 2024-12-04
Type: Initial release

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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.