6JK8
Cryo-EM structure of the full-length human IGF-1R in complex with insulin
- PDB DOI: https://doi.org/10.2210/pdb6JK8/pdb
- EM Map EMD-9838: EMDB EMDataResource
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2019-02-27 Released: 2020-03-04 
- Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 5.00 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. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Insulin-like growth factor 1 receptor | 1,367 | Homo sapiens | Mutation(s): 0  Gene Names: IGF1R EC: 2.7.10.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069 | |||||
PHAROS:  P08069 GTEx:  ENSG00000140443  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P08069 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Insulin | 110 | Homo sapiens | Mutation(s): 0  Gene Names: INS | ||
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 AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
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, G, H, I | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81874LD GlyCosmos:  G81874LD GlyGen:  G81874LD |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | J [auth A] K [auth A] L [auth A] M [auth B] N [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 5.00 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | 3.0.4 |
Entry History & Funding Information
Deposition Data
Funding Organization | Location | Grant Number |
---|---|---|
Ministry of Science and Technology (China) | China | 2018YFA0507103 |
National Natural Science Foundation of China | China | 31870719 |
National Natural Science Foundation of China | China | 11774011 |
Revision History (Full details and data files)
- Version 1.0: 2020-03-04
Type: Initial release - Version 1.1: 2020-03-25
Changes: Database references - Version 1.2: 2020-04-22
Changes: Database references - Version 1.3: 2020-05-20
Changes: Database references, Derived calculations - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary