[English] 日本語
Yorodumi
- PDB-7e7e: The co-crystal structure of ACE2 with Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e7e
TitleThe co-crystal structure of ACE2 with Fab
Components
  • (h11B11-Fab) x 2
  • Processed angiotensin-converting enzyme 2
KeywordsANTIVIRAL PROTEIN / ACE2 Fab
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / regulation of vasoconstriction / peptidyl-dipeptidase activity / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / viral translation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXiao, J.Y. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2021
Title: A broadly neutralizing humanized ACE2-targeting antibody against SARS-CoV-2 variants.
Authors: Du, Y. / Shi, R. / Zhang, Y. / Duan, X. / Li, L. / Zhang, J. / Wang, F. / Zhang, R. / Shen, H. / Wang, Y. / Wu, Z. / Peng, Q. / Pan, T. / Sun, W. / Huang, W. / Feng, Y. / Feng, H. / Xiao, J. ...Authors: Du, Y. / Shi, R. / Zhang, Y. / Duan, X. / Li, L. / Zhang, J. / Wang, F. / Zhang, R. / Shen, H. / Wang, Y. / Wu, Z. / Peng, Q. / Pan, T. / Sun, W. / Huang, W. / Feng, Y. / Feng, H. / Xiao, J. / Tan, W. / Wang, Y. / Wang, C. / Yan, J.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
H: h11B11-Fab
L: h11B11-Fab
B: Processed angiotensin-converting enzyme 2
C: h11B11-Fab
D: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,9338
Polymers237,8026
Non-polymers1312
Water00
1
A: Processed angiotensin-converting enzyme 2
H: h11B11-Fab
L: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9664
Polymers118,9013
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Processed angiotensin-converting enzyme 2
C: h11B11-Fab
D: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9664
Polymers118,9013
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.779, 115.462, 224.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 70386.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Comamonas sp. Hi5 (bacteria) / References: UniProt: Q9BYF1
#2: Antibody h11B11-Fab


Mass: 24955.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pseudoalteromonas sp. AB293f (bacteria)
#3: Antibody h11B11-Fab


Mass: 23558.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pseudoalteromonas sp. AB293f (bacteria)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate(pH 6.5),30% (v/v) PEG 550

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 48694 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.415 / Net I/σ(I): 5.5
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 1.739 / Num. unique obs: 2472

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4L

1r4l


Resolution: 3.8→49.84 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.327 1284 4.98 %
Rwork0.2755 24504 -
obs0.2781 25788 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.13 Å2 / Biso mean: 118.6854 Å2 / Biso min: 36.09 Å2
Refinement stepCycle: final / Resolution: 3.8→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16055 0 2 0 16057
Biso mean--148.4 --
Num. residues----2016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.950.45581340.38762561269595
3.95-4.130.43331410.350126862827100
4.13-4.350.41311410.31262682282399
4.35-4.620.33281430.284626982841100
4.62-4.980.36171410.27727132854100
4.98-5.480.32331450.261227312876100
5.48-6.270.3351410.290227462887100
6.27-7.890.28981460.26227782924100
7.89-49.840.23571520.20962909306199
Refinement TLS params.Method: refined / Origin x: -66.4715 Å / Origin y: 10.4899 Å / Origin z: -23.6932 Å
111213212223313233
T0.4002 Å20.0218 Å2-0.0312 Å2-0.4787 Å20.0085 Å2--0.4792 Å2
L0.014 °2-0.0398 °20.0042 °2-0.0652 °20.0521 °2--0.1106 °2
S0.0296 Å °-0.0201 Å °-0.0274 Å °-0.032 Å °-0.0131 Å °-0.0263 Å °0.0018 Å °0.0309 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 803
2X-RAY DIFFRACTION1allH1 - 217
3X-RAY DIFFRACTION1allL1 - 210
4X-RAY DIFFRACTION1allB19 - 803
5X-RAY DIFFRACTION1allC1 - 217
6X-RAY DIFFRACTION1allD1 - 210

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more