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- PDB-8zmn: Crystal structure of ANTXR1 -

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Basic information

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


filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / actin filament binding / transmembrane signaling receptor activity / actin cytoskeleton organization / external side of plasma membrane ...filopodium membrane / negative regulation of extracellular matrix assembly / blood vessel development / lamellipodium membrane / collagen binding / substrate adhesion-dependent cell spreading / actin filament binding / transmembrane signaling receptor activity / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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