6TM2 | pdb_00006tm2

Human MUC2 AAs 21-1397

PDB DOI: https://doi.org/10.2210/pdb6TM2/pdb
EM Map EMD-10517: EMDB EMDataResource

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

Deposited: 2019-12-03 Released: 2020-10-21
Deposition Author(s): Javitt, G., Khmelnitsky, L., Albert, L., Elad, N., Ilani, T., Diskin, R., Fass, D.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Assembly Mechanism of Mucin and von Willebrand Factor Polymers.

Javitt, G., Khmelnitsky, L., Albert, L., Bigman, L.S., Elad, N., Morgenstern, D., Ilani, T., Levy, Y., Diskin, R., Fass, D.

(2020) Cell 183: 717

PubMed: 33031746 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2020.09.021
Primary Citation Related Structures:
6TM2, 6TM6, 7A5O

PubMed Abstract:
The respiratory and intestinal tracts are exposed to physical and biological hazards accompanying the intake of air and food. Likewise, the vasculature is threatened by inflammation and trauma. Mucin glycoproteins and the related von Willebrand factor guard the vulnerable cell layers in these diverse systems. Colon mucins additionally house and feed the gut microbiome. Here, we present an integrated structural analysis of the intestinal mucin MUC2. Our findings reveal the shared mechanism by which complex macromolecules responsible for blood clotting, mucociliary clearance, and the intestinal mucosal barrier form protective polymers and hydrogels. Specifically, cryo-electron microscopy and crystal structures show how disulfide-rich bridges and pH-tunable interfaces control successive assembly steps in the endoplasmic reticulum and Golgi apparatus. Remarkably, a densely O-glycosylated mucin domain performs an organizational role in MUC2. The mucin assembly mechanism and its adaptation for hemostasis provide the foundation for rational manipulation of barrier function and coagulation.

Organizational Affiliation

Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecule Content

Total Structure Weight: 307.96 kDa
Atom Count: 18,418
Modeled Residue Count: 2,410
Deposited Residue Count: 2,766
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-2	A, B	729	Homo sapiens	Mutation(s): 0 Gene Names: MUC2, SMUC
UniProt & NIH Common Fund Data Resources
Find proteins for Q02817 (Homo sapiens) Explore Q02817 Go to UniProtKB: Q02817
PHAROS: Q02817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02817
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q02817-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-2	C, D	448	Homo sapiens	Mutation(s): 0 Gene Names: MUC2, SMUC
UniProt & NIH Common Fund Data Resources
Find proteins for Q02817 (Homo sapiens) Explore Q02817 Go to UniProtKB: Q02817
PHAROS: Q02817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02817
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain D	Go to GlyGen: Q02817-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-2	E, F	206	Homo sapiens	Mutation(s): 0 Gene Names: MUC2, SMUC
UniProt & NIH Common Fund Data Resources
Find proteins for Q02817 (Homo sapiens) Explore Q02817 Go to UniProtKB: Q02817
PHAROS: Q02817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02817
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	2		N-Glycosylation	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	K [auth A], L [auth A], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain J [auth A]	I [auth A] J [auth A] M [auth B] N [auth B] Q [auth C] I [auth A], J [auth A], M [auth B], N [auth B], Q [auth C], R [auth D], S [auth E], T [auth E], U [auth F], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2020-10-28
Changes: Database references
Version 1.2: 2020-11-11
Changes: Database references
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary