8VS6

L-TGF-b3/avb8

PDB DOI: https://doi.org/10.2210/pdb8VS6/pdb
EM Map EMD-43489: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Cricetulus griseus
Mutation(s): No

Deposited: 2024-01-23 Released: 2024-09-11
Deposition Author(s): Jin, M., Cheng, Y., Nishimura, S.L.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Dynamic allostery drives autocrine and paracrine TGF-beta signaling

Jin, M., Cheng, Y., Nishimura, S.L.

(2024) Cell

Macromolecule Content

Total Structure Weight: 226.16 kDa
Atom Count: 6,438
Modelled Residue Count: 800
Deposited Residue Count: 1,993
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming growth factor beta-3 proprotein	A [auth E]	389	Homo sapiens	Mutation(s): 0 Gene Names: TGFB3
UniProt & NIH Common Fund Data Resources
Find proteins for P10600 (Homo sapiens) Explore P10600 Go to UniProtKB: P10600
PHAROS: P10600 GTEx: ENSG00000119699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10600
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	B [auth A]	962	Homo sapiens	Mutation(s): 0 Gene Names: ITGAV, MSK8, VNRA, VTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756 Go to UniProtKB: P06756
PHAROS: P06756 GTEx: ENSG00000138448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06756
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B [auth A]	Go to GlyGen: P06756-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-8	C [auth B]	642	Homo sapiens	Mutation(s): 0 Gene Names: ITGB8
UniProt & NIH Common Fund Data Resources
Find proteins for P26012 (Homo sapiens) Explore P26012 Go to UniProtKB: P26012
PHAROS: P26012 GTEx: ENSG00000105855
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26012
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain C [auth B]	Go to GlyGen: P26012-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	6		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], F, G, H	2		N-Glycosylation	Interactions Focus chain E [auth D] Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E [auth D] Focus chain F Focus chain G Focus chain H

Small Molecules

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