6M17
The 2019-nCoV RBD/ACE2-B0AT1 complex
- PDB DOI: https://doi.org/10.2210/pdb6M17/pdb
- EM Map EMD-30039: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN/VIRAL PROTEIN
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
- Expression System: Homo sapiens
- Mutation(s): No
- Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc
- Deposited: 2020-02-24 Released: 2020-03-11
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.90 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 3.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Sodium-dependent neutral amino acid transporter B(0)AT1 | A, D [auth C] | 654 | Homo sapiens | Mutation(s): 0 Gene Names: SLC6A19, B0AT1 Membrane Entity: Yes |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q695T7 (Homo sapiens) Explore Q695T7 Go to UniProtKB: Q695T7 | |||||
PHAROS: Q695T7 GTEx: ENSG00000174358 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q695T7 | ||||
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 |
| Angiotensin-converting enzyme 2 | B, E [auth D] | 814 | Homo sapiens | Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data) Membrane Entity: Yes |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1 | |||||
PHAROS: Q9BYF1 GTEx: ENSG00000130234 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9BYF1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S1 | C [auth E], F | 223 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: S, 2 Membrane Entity: Yes |  |
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G, H, I, J, K G, H, I, J, K, L, M, O, P, Q, R, S, T, U | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | N, V | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG (Subject of Investigation/LOI) Query on NAG | BA [auth B] DA [auth C] EA [auth C] FA [auth C] GA [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| LEU (Subject of Investigation/LOI) Query on LEU | AA [auth A], HA [auth C] | LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | CA [auth B], JA [auth D] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.90 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | 2.13.2 |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-03-11 Deposition Author(s): Yan, R.H., Zhang, Y.Y., Li, Y.N., Xia, L., Guo, Y.Y., Zhou, Q.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 31971123 |
| National Natural Science Foundation of China (NSFC) | China | 81920108015 |
| National Natural Science Foundation of China (NSFC) | China | 31930059 |
Revision History (Full details and data files)
- Version 1.0: 2020-03-11
Type: Initial release - Version 1.1: 2020-03-18
Changes: Database references - Version 1.2: 2020-04-01
Changes: Source and taxonomy, Structure summary - Version 1.3: 2020-04-08
Changes: Database references - Version 1.4: 2020-04-29
Changes: Structure summary - Version 1.5: 2020-05-06
Changes: Database references, Source and taxonomy, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.0: 2020-11-04
Type: Coordinate replacement
Reason: Model completeness
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary - Version 3.1: 2021-03-10
Changes: Structure summary
