9NHX | pdb_00009nhx

The cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis

PDB DOI: https://doi.org/10.2210/pdb9NHX/pdb
EM Map EMD-49433: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Neisseria meningitidis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-25 Released: 2026-09-02
Deposition Author(s): Dubey, S., Noinaj, N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NHX

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

Literature

The cryo-EM structure of the periplasmic chaperone Skp from Neisseria meningitidis

Dubey, S., Noinaj, N.

To be published.

Macromolecule Content

Total Structure Weight: 103.03 kDa
Atom Count: 6,732
Modeled Residue Count: 840
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein OmpH, putative	A, B, C, D, E A, B, C, D, E, F	147	Neisseria meningitidis	Mutation(s): 0 Gene Names: skp, CNQ34_05000, COI09_03455, ERS514591_00664, ERS514851_00425, NCTC8554_02345
UniProt
Find proteins for A0A0Y6QFF4 (Neisseria meningitidis) Explore A0A0Y6QFF4 Go to UniProtKB: A0A0Y6QFF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0Y6QFF4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18rc1_3777:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127884

Revision History (Full details and data files)

Version 1.0: 2026-09-02
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.