[English] 日本語
Yorodumi
- PDB-6zpq: Crystal structure of the open conformation of Angiotensin-1 conve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zpq
TitleCrystal structure of the open conformation of Angiotensin-1 converting enzyme N-domain.
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / Open conformation / metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly / hormone catabolic process / bradykinin catabolic process / metallodipeptidase activity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / neutrophil mediated immunity / hormone metabolic process / mitogen-activated protein kinase binding / mitogen-activated protein kinase kinase binding / chloride ion binding / arachidonate secretion / post-transcriptional regulation of gene expression / peptide catabolic process / heart contraction / positive regulation of systemic arterial blood pressure / regulation of heart rate by cardiac conduction / antigen processing and presentation of peptide antigen via MHC class I / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / amyloid-beta metabolic process / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / regulation of vasoconstriction / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / blood vessel diameter maintenance / angiotensin-activated signaling pathway / kidney development / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / calmodulin binding / lysosome / endosome / negative regulation of gene expression / external side of plasma membrane / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
BORIC ACID / 2-METHOXYETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026647/1 United Kingdom
CitationJournal: Febs J. / Year: 2021
Title: Angiotensin-converting enzyme open for business: structural insights into the subdomain dynamics.
Authors: Cozier, G.E. / Lubbe, L. / Sturrock, E.D. / Acharya, K.R.
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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: Angiotensin-converting enzyme
B: Angiotensin-converting enzyme
C: Angiotensin-converting enzyme
D: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,36966
Polymers290,4264
Non-polymers7,94362
Water30,0851670
1
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,99520
Polymers72,6071
Non-polymers2,38919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63018
Polymers72,6071
Non-polymers2,02417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,25413
Polymers72,6071
Non-polymers1,64712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,49015
Polymers72,6071
Non-polymers1,88314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.683, 99.934, 128.701
Angle α, β, γ (deg.)97.756, 90.206, 111.057
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 72606.508 Da / Num. of mol.: 4
Mutation: N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A

-
Sugars , 3 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#13: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 12 types, 1724 molecules

#4: Chemical
ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: BH3O3
#5: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#10: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#12: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#14: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#15: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1670 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent Cations, 30% PEG550MME/PEG20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→96.26 Å / Num. obs: 286723 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Net I/σ(I): 7.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 14077 / CC1/2: 0.546 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9V

6f9v


Resolution: 1.85→80.5 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.1773 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2136 2024 71 %
Rwork0.1844 283870 -
obs0.1846 285894 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.45 Å2
Refinement stepCycle: LAST / Resolution: 1.85→80.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19818 0 497 1670 21985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008721197
X-RAY DIFFRACTIONf_angle_d0.772828853
X-RAY DIFFRACTIONf_chiral_restr0.04782988
X-RAY DIFFRACTIONf_plane_restr0.00583733
X-RAY DIFFRACTIONf_dihedral_angle_d18.300212420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.38021390.334419878X-RAY DIFFRACTION95.56
1.9-1.950.36511530.317119982X-RAY DIFFRACTION95.9
1.95-20.29291250.292719999X-RAY DIFFRACTION96.18
2-2.070.32541560.262520099X-RAY DIFFRACTION96.55
2.07-2.140.26991250.248220159X-RAY DIFFRACTION96.75
2.14-2.230.28181340.229220181X-RAY DIFFRACTION97.08
2.23-2.330.2761430.213620287X-RAY DIFFRACTION97.25
2.33-2.450.25041440.195120236X-RAY DIFFRACTION97.65
2.45-2.610.22471340.183120358X-RAY DIFFRACTION97.87
2.61-2.810.20911790.179320421X-RAY DIFFRACTION98.08
2.81-3.090.20971400.183120487X-RAY DIFFRACTION98.44
3.09-3.540.22771600.175520536X-RAY DIFFRACTION98.7
3.54-4.460.16021480.143420576X-RAY DIFFRACTION99.05
4.46-80.50.15431440.149620671X-RAY DIFFRACTION99.31

+
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