[English] 日本語
Yorodumi
- PDB-8zmn: Crystal structure of ANTXR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zmn
TitleCrystal structure of ANTXR1
ComponentsAnthrax toxin receptor 1
KeywordsTOXIN / Toxin receptor
Function / homology
Function and homology information


reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / transmembrane signaling receptor activity / actin filament binding / actin cytoskeleton organization ...reproductive process / filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / transmembrane signaling receptor activity / actin filament binding / actin cytoskeleton organization / external side of plasma membrane / cell surface / metal ion binding / plasma membrane
Similarity search - Function
Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Anthrax toxin receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsZheng, H. / Hu, J. / Fu, L. / Chen, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of Anthrax toxin receptor 1 APO from Rattus norvegicus
Authors: Zheng, H. / Chen, R.
History
DepositionMay 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anthrax toxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1762
Polymers21,1531
Non-polymers231
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.516, 39.224, 102.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Anthrax toxin receptor 1


Mass: 21152.758 Da / Num. of mol.: 1 / Mutation: C175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Antxr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0PMD2
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 28% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.14→36.64 Å / Num. obs: 7809 / % possible obs: 85.96 % / Redundancy: 8.3 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1537 / Net I/σ(I): 9.96
Reflection shellResolution: 2.14→2.217 Å / Redundancy: 7 % / Rmerge(I) obs: 1.007 / Num. unique obs: 5973 / CC1/2: 0.693 / CC star: 0.905 / % possible all: 98.38

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→36.64 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.0255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2632 366 4.7 %
Rwork0.21 7429 -
obs0.2126 7795 85.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.31 Å2
Refinement stepCycle: LAST / Resolution: 2.14→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 1 34 1528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681527
X-RAY DIFFRACTIONf_angle_d0.7482060
X-RAY DIFFRACTIONf_chiral_restr0.0465218
X-RAY DIFFRACTIONf_plane_restr0.0081269
X-RAY DIFFRACTIONf_dihedral_angle_d15.1521558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.450.3289950.26012196X-RAY DIFFRACTION77.58
2.45-3.090.31681420.24432520X-RAY DIFFRACTION89.48
3.09-36.640.22291290.18272713X-RAY DIFFRACTION90.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0182505645-0.04315668199560.5703089923882.719033795040.2275905939762.2557188126-0.0138731453189-0.00916648521055-0.02292867556910.112752792470.01113511452230.143725791444-0.10980588677-0.164192099863-0.0007068978129120.1580747712670.01540146184570.04393431704840.153445620908-0.01571918297290.174288140611-18.21743663465.82312493594-12.6666787781
22.26897841432-0.3385280416680.6966332397331.824882359540.856441284760.991430023015-0.07935769403280.241406172510.048677462282-0.8289441662590.05615680608670.2890283743490.699534187697-0.05392534711610.07817423858330.250419508573-0.06336934555140.01735466956010.204689552344-0.02235068894310.145098626405-11.2820483205-1.07931819789-23.1749830436
31.89629324707-0.227570199161-0.779025813432.85277546021.225991482282.22649813315-0.00757602611897-0.003077894228710.02581678985380.3438526583770.174714174998-0.1889754422670.2126898798640.28526233233-0.1431213486730.183124893250.00453497266181-0.003645404949740.211122703576-0.009813088289320.20095623788-5.65924908915-1.43017074873-10.7101016242
43.952041177321.079460357120.5912989851165.50500171432-0.9242322600233.26633629517-0.018703934818-1.08775305735-0.086104885110.318382805833-0.223208173313-1.267567363560.4679759875930.674576722625-0.04321012775270.2720795347420.0323812932622-0.1120632318730.242885111288-0.09866397890130.421984165319-4.4158874196515.3095480571-9.0394520085
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 35 through 117 )35 - 1171 - 83
22chain 'A' and (resid 118 through 134 )118 - 13484 - 100
33chain 'A' and (resid 135 through 201 )135 - 201101 - 167
44chain 'A' and (resid 202 through 218 )202 - 218168 - 184

+
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://pdbjlvh1.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