8E7M | pdb_00008e7m

Structure of the human ACE2 receptor in complex with antibody Fab fragment, 05B04

PDB DOI: https://doi.org/10.2210/pdb8E7M/pdb
EM Map EMD-27939: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-08-24 Released: 2022-09-28
Deposition Author(s): Barnes, C.O.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Human anti-ACE2 monoclonal antibodies as pan-sarbecovirus prophylactic agents

Zhang, F., Jenkins, J., de Carvalho, R.V., Nakandakari-Higa, S., Chen, T., Abernathy, M.E., Nyakatura, E., Andrew, D., Lebedeva, I., Lorenz, I.C., Hoffmann, H.H., Rice, C.M., Victora, G.D., Barnes, C.O., Haziioannou, T., Bieniasz, P.D.

(2022) bioRxiv

DOI: https://doi.org/10.1101/2022.08.24.505169

Macromolecule Content

Total Structure Weight: 122.03 kDa
Atom Count: 8,293
Modeled Residue Count: 1,030
Deposited Residue Count: 1,067
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	626	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
05B04 Heavy Chain	B [auth H]	227	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
05B04 Light Chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	2		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
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 I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-28

Deposition Author(s):

Barnes, C.O.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	GT15335

Revision History (Full details and data files)

Version 1.0: 2022-09-28
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Refinement description, Structure summary