7Y76

SIT1-ACE2-BA.5 RBD

PDB DOI: https://doi.org/10.2210/pdb7Y76/pdb
EM Map EMD-33653: EMDB EMDataResource

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2022-06-21 Released: 2023-01-04
Deposition Author(s): Shen, Y.P., Li, Y.N., Zhang, Y.Y., Yan, R.H.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2.

Shen, Y., Wang, J., Li, Y., Zhang, Y., Tian, R., Yan, R.

(2022) Cell Discov 8: 123-123

PubMed: 36384914 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00488-x
Primary Citation of Related Structures:
7Y75, 7Y76

Organizational Affiliation

Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.

Macromolecule Content

Total Structure Weight: 396.67 kDa
Atom Count: 25,180
Modelled Residue Count: 3,042
Deposited Residue Count: 3,382
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIT1	A [auth B], D	613	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP91 (Homo sapiens) Explore Q9NP91 Go to UniProtKB: Q9NP91
PHAROS: Q9NP91 GTEx: ENSG00000163817
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NP91
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A [auth B] Focus chain D	Go to GlyGen: Q9NP91-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	B [auth A], E [auth C]	826	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
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain B [auth A] Focus chain E [auth C]	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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	252	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth E] Focus chain F	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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, N, O, P, Q, R, S, T, U, V	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PH (Subject of Investigation/LOI) Query on 3PH Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] FA [auth D] GA [auth D] HA [auth D] Y [auth B] AA [auth B], FA [auth D], GA [auth D], HA [auth D], Y [auth B], Z [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain IA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	BA [auth A] DA [auth D] EA [auth D] IA [auth C] W [auth B] BA [auth A], DA [auth D], EA [auth D], IA [auth C], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth A] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain IA [auth C] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth A] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain IA [auth C] Focus chain W [auth B] Focus chain X [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain JA [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain JA [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain JA [auth C]	CA [auth A], JA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain JA [auth C] Interactions & Density Focus chain CA [auth A] Focus chain JA [auth C]