8U4K

Structure of the HER2/HER4/BTC Heterodimer Extracellular Domain

PDB DOI: https://doi.org/10.2210/pdb8U4K/pdb
EM Map EMD-41885: EMDB EMDataResource

Classification: MEMBRANE PROTEIN, TRANSFERASE
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-10 Released: 2024-03-13
Deposition Author(s): Trenker, R., Diwanji, D., Bingham, T., Verba, K.A., Jura, N.
Funding Organization(s): German Research Foundation (DFG), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.27 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

Structure of the HER2/HER4/BTC Heterodimer Extracellular Domain

Trenker, R., Diwanji, D., Bingham, T., Verba, K.A., Jura, N.

To be published.

Macromolecule Content

Total Structure Weight: 147.28 kDa
Atom Count: 9,989
Modelled Residue Count: 1,228
Deposited Residue Count: 1,263
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform JM-A CYT-1 of Receptor tyrosine-protein kinase erbB-4	A	609	Homo sapiens	Mutation(s): 0 Gene Names: ERBB4, HER4 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15303 (Homo sapiens) Explore Q15303 Go to UniProtKB: Q15303
PHAROS: Q15303 GTEx: ENSG00000178568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15303
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	B	606	Homo sapiens	Mutation(s): 0 Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626 Go to UniProtKB: P04626
PHAROS: P04626 GTEx: ENSG00000141736
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04626
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Betacellulin	C	48	Homo sapiens	Mutation(s): 0 Gene Names: BTC
UniProt & NIH Common Fund Data Resources
Find proteins for P35070 (Homo sapiens) Explore P35070 Go to UniProtKB: P35070
PHAROS: P35070 GTEx: ENSG00000174808
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35070
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, I, K, L	3		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, M	2		N-Glycosylation	Interactions Focus chain J Focus chain M Interactions & Density Focus chain J Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B]	N [auth A], O [auth A], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	TR 1668/1-1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM139636
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA274502