6CE9

Insulin Receptor ectodomain in complex with two insulin molecules

PDB DOI: https://doi.org/10.2210/pdb6CE9/pdb
EM Map EMD-7462: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, Ovis aries
Expression System: Mus musculus
Mutation(s): No

Deposited: 2018-02-11 Released: 2018-03-14
Deposition Author(s): Scapin, G., Dandey, V.P., Zhang, Z., Strickland, C., Potter, C.S., Carragher, B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD), Simons Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 234.31 kDa
Atom Count: 10,782
Modelled Residue Count: 1,286
Deposited Residue Count: 1,996
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin receptor	A, B	917	Homo sapiens	Mutation(s): 0 Gene Names: INSR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens) Explore P06213 Go to UniProtKB: P06213
PHAROS: P06213 GTEx: ENSG00000171105
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06213
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin receptor	C [auth M], H [auth P]	30	Homo sapiens	Mutation(s): 0 Gene Names: INSR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens) Explore P06213 Go to UniProtKB: P06213
PHAROS: P06213 GTEx: ENSG00000171105
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06213
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	D [auth K], F [auth N]	21	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308 Go to UniProtKB: P01308
PHAROS: P01308 GTEx: ENSG00000254647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	E [auth L], G [auth O]	30	Ovis aries	Mutation(s): 0
UniProt
Find proteins for P01318 (Ovis aries) Explore P01318 Go to UniProtKB: P01318
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01318
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth C], K [auth E], N [auth H], P [auth J]	3		N-Glycosylation	Interactions Focus chain I [auth C] Focus chain K [auth E] Focus chain N [auth H] Focus chain P [auth J] Interactions & Density Focus chain I [auth C] Focus chain K [auth E] Focus chain N [auth H] Focus chain P [auth J]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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	J [auth D], O [auth I]	3		N-Glycosylation	Interactions Focus chain J [auth D] Focus chain O [auth I] Interactions & Density Focus chain J [auth D] Focus chain O [auth I]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth F], Q	2		N-Glycosylation	Interactions Focus chain L [auth F] Focus chain Q Interactions & Density Focus chain L [auth F] Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], R	2		N-Glycosylation	Interactions Focus chain M [auth G] Focus chain R Interactions & Density Focus chain M [auth G] Focus chain R
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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 S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	S [auth A], T [auth A], U [auth B], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	0.6.5

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103310
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	OD019994
Simons Foundation	United States	349247

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-03-21
Changes: Database references
Version 1.2: 2018-04-18
Changes: Data collection, Database references
Version 1.3: 2019-12-18
Changes: Author supporting evidence, Data collection, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary