8OER | pdb_00008oer

MUC5B amino acids 26-1435

PDB DOI: https://doi.org/10.2210/pdb8OER/pdb
EM Map EMD-16808: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-03-12 Released: 2024-03-27
Deposition Author(s): Khmelnitsky, L., Fass, D.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8OER

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

Literature

Pulmonary Fibrosis Linked to Impaired Mucin 5B Supramolecular Assembly

Khmelnitsky, L., Javitt, G., Reznik, N., Yeshaya, N., Elad, N., Anikster, Y., Shalva, N., Barel, O., Pode-Shakked, B., Greenberg, L.J., Segel, M.J., Fass, D.

To be published.

Macromolecule Content

Total Structure Weight: 288.5 kDa
Atom Count: 19,282
Modeled Residue Count: 2,536
Deposited Residue Count: 2,640
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-5B	A, B	760	Homo sapiens	Mutation(s): 0 Gene Names: MUC5B, MUC5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC84 (Homo sapiens) Explore Q9HC84 Go to UniProtKB: Q9HC84
PHAROS: Q9HC84 GTEx: ENSG00000117983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC84
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9HC84-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-5B	C, D	460	Homo sapiens	Mutation(s): 0 Gene Names: MUC5B, MUC5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC84 (Homo sapiens) Explore Q9HC84 Go to UniProtKB: Q9HC84
PHAROS: Q9HC84 GTEx: ENSG00000117983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC84
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: Q9HC84-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-5B	E [auth I], F [auth J]	100	Homo sapiens	Mutation(s): 0 Gene Names: MUC5B, MUC5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC84 (Homo sapiens) Explore Q9HC84 Go to UniProtKB: Q9HC84
PHAROS: Q9HC84 GTEx: ENSG00000117983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] M [auth B] G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth I] SDF format, chain W [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth I] MOL2 format, chain W [auth J] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth I] mmCIF format, chain W [auth J]	K [auth A] L [auth A] Q [auth B] R [auth B] T [auth C] K [auth A], L [auth A], Q [auth B], R [auth B], T [auth C], U [auth D], V [auth I], W [auth J]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth I] Focus chain W [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth I] Focus chain W [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Khmelnitsky, L.

Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	2660/20

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary
Version 1.2: 2025-07-09
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.