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- PDB-8fz4: The von Willebrand factor A domain of Anthrax toxin receptor 2 -

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Basic information

Entry
Database: PDB / ID: 8fz4
TitleThe von Willebrand factor A domain of Anthrax toxin receptor 2
ComponentsAnthrax toxin receptor 2
KeywordsMEMBRANE PROTEIN / CMG2 / anthrax toxin receptor / MIDAS domain
Function / homology
Function and homology information


Uptake and function of anthrax toxins / transmembrane signaling receptor activity / endosome membrane / endoplasmic reticulum membrane / cell surface / extracellular region / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPedroza-Romo, M.J. / Soleimani, S. / Lewis, A. / Smith, T. / Brown, S. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-01 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits.
Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, ...Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, T. / Lebedev, A. / Moody, J.D.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthrax toxin receptor 2
B: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5816
Polymers39,4612
Non-polymers1204
Water1,74797
1
A: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7903
Polymers19,7311
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7903
Polymers19,7311
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.244, 88.969, 59.779
Angle α, β, γ (deg.)90.000, 128.130, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Anthrax toxin receptor 2 / Capillary morphogenesis gene 2 protein / CMG-2


Mass: 19730.570 Da / Num. of mol.: 2 / Mutation: P37G, C39A, C175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANTXR2, CMG2 / Plasmid: pET42_SUMO / Details (production host): Kanamycin resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: P58335
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.76 % / Description: Rhomboid plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.2 uL of 20 mg/mL protein in 12.5 mM Tris pH 8.8, 200mM KCl, 10mM MgCl2 combined with 1.2 uL of 0.1 M Glycine pH 9.5, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.19→39.08 Å / Num. obs: 16416 / % possible obs: 98.56 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.44 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08972 / Rpim(I) all: 0.0365 / Rrim(I) all: 0.09702 / Net I/σ(I): 10.8
Reflection shellResolution: 2.19→2.268 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8622 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 1620 / CC1/2: 0.849 / CC star: 0.958 / Rpim(I) all: 0.3496 / Rrim(I) all: 0.9318 / % possible all: 98.96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
autoPROCdata scaling
Coot0.9.6 ELmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→39.08 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 784 4.78 %
Rwork0.2175 15632 -
obs0.2193 16416 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.33 Å2
Refinement stepCycle: LAST / Resolution: 2.19→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 4 97 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232547
X-RAY DIFFRACTIONf_angle_d0.47123465
X-RAY DIFFRACTIONf_chiral_restr0.0405411
X-RAY DIFFRACTIONf_plane_restr0.0034451
X-RAY DIFFRACTIONf_dihedral_angle_d10.6178863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.330.34291470.31132572X-RAY DIFFRACTION98.69
2.33-2.510.33041440.27212545X-RAY DIFFRACTION96.94
2.51-2.760.29631290.24312602X-RAY DIFFRACTION99.56
2.76-3.160.26231230.22912635X-RAY DIFFRACTION99.28
3.16-3.980.23761090.20732624X-RAY DIFFRACTION98.17
3.98-39.080.22021320.18562654X-RAY DIFFRACTION98.9
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)
11.187435433430.4971154855471.128931919883.954705219652.154940597593.21422901009-0.02508977941410.114822067307-0.4983921666510.1773040120630.142206861104-0.3396307188540.5387777717260.319087157754-0.16339689780.7489233115990.05670230667920.3973496316610.317011584205-0.007378500019360.6952193302611.58239214047-12.319312521521.2888352924
22.072461131611.557138780091.035381991642.25733865961-0.3495022098544.57801648976-0.1309682790340.2447574287720.0291560857646-0.311583077750.333688479707-0.2119614296330.2946493580070.0323097988029-0.1863703496860.580204848089-0.04053705875950.3578660347750.289597891265-0.04808263859940.695427837809-1.20075275084-3.7325154745116.8605242081
31.25810363117-0.105937672659-0.8180552328362.05193761958-0.8651028862213.19497978803-0.173579798083-0.278706512934-0.2390091027150.1386455443720.0393603253758-0.0008615218126580.1474230766390.3516264389880.1230279464310.573277223101-0.02126175057760.4045434197910.329769029361-0.007871151082290.691377460531.26435651412-6.4970706166631.6058923159
42.35242762688-0.8553056836741.166065432093.710379600660.05223372667490.649097636226-0.276105995281.46333362438-0.876905455911-0.8736932248480.0118519133129-0.8455587204040.713896097820.7227725768650.5030655662930.858937757355-0.08742296531440.5697490707040.961316398897-0.1071239898621.2585070969814.4857396973-8.2435325160522.9724283843
53.719757182261.436308867320.7411941246724.553032490040.9978832929712.70827117868-0.07218115569770.5583794287130.521691847274-0.363724892184-0.356849070325-0.225424318128-0.3901304993550.2394630547370.1275941272370.5330920516850.01182934441920.4569479878970.311927013049-0.06635251335460.7944530876822.448637384321.19059024291.05062852982
64.479633625660.531490205943-1.077329627765.76771937943-1.61239525225.8801151682-0.09680047217570.706010649518-0.160780618419-0.1497051733390.0226472741116-0.6644215407150.1423758967690.3826957479690.07628535904610.476238149568-7.54434385926E-50.3254005192520.387533337412-0.05626476079060.70121759742925.25718073029.58359822952-6.26038643406
72.20636789608-0.7421111735960.8391299747222.879364391572.616383407443.452677641850.1439738860310.1423661738080.0208347581871-0.1856441101040.226424955992-0.701483884724-0.3501299447510.590851985709-0.3489481240370.5521435481480.005851083296080.3222643824710.351805479551-0.1144137283240.78393931669428.907139250315.76973924844.05877872528
83.65467388745-0.0780123875347-0.1248878413410.161647013662-0.373636550022.886620394390.0564359239449-0.1621065311590.01635330750320.4012064633680.03020231134460.06606070925780.0336210632767-0.015811498994-0.09713277781560.508491932994-0.02520039422580.3366341019360.27316879958-0.03347805459190.61856753702216.276130572212.76973282035.8688554945
91.12523575122.43793301422-0.4881076318436.26756788792-0.5132277630641.09308404314-0.01562143003840.1366358342550.4305647490490.0121497114377-0.03577122675630.6640132464960.0782148454109-0.6493403298040.07242065460380.4203596119960.04323034305220.4531403910510.286892259238-0.05420448609310.6994844566336.9596806243115.75967677237.09963564437
101.25052757336-0.83967090248-1.141402773510.5539848264470.8352829638113.917358699080.04849732542670.489303887118-0.0726402852131-0.3404450288290.0802475136850.508791912795-0.339140442009-0.9359626789470.003193695073150.521975516862-0.01639136242270.4331395645510.5423220938060.04696452706350.66092894201810.027969527815.0548913855-3.78889211195
112.20092728027-0.5454241253171.55297552675.244333579890.8334727038864.14124379934-0.06587566326070.8200662198970.213495511818-0.2743348796120.113455032886-0.373371493752-0.5945277474820.128811326316-0.1423453267350.6817495363620.001292219432830.7821236822040.4443982227380.1428329378240.5882712834414.540035905616.8243526056-10.6927364326
122.8421312113-0.453434642389-1.894723897890.368618720683-0.5122770857733.534164510790.7003672106380.1855103985151.23815074951-0.7967919026030.334294947457-0.361390372547-1.094418976170.101497748634-0.938520687250.681476798494-0.2443945215170.2052797314770.792877480360.1853261138881.1078609856620.265080249523.4580189378-10.8756026803
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 38 through 52 )AA38 - 521 - 15
22chain 'A' and (resid 53 through 119 )AA53 - 11916 - 82
33chain 'A' and (resid 120 through 192 )AA120 - 19283 - 155
44chain 'A' and (resid 193 through 214 )AA193 - 214156 - 177
55chain 'B' and (resid 38 through 52 )BB38 - 521 - 15
66chain 'B' and (resid 53 through 72 )BB53 - 7216 - 35
77chain 'B' and (resid 73 through 110 )BB73 - 11036 - 73
88chain 'B' and (resid 111 through 154 )BB111 - 15474 - 117
99chain 'B' and (resid 155 through 168 )BB155 - 168118 - 131
1010chain 'B' and (resid 169 through 192 )BB169 - 192132 - 155
1111chain 'B' and (resid 193 through 202 )BB193 - 202156 - 165
1212chain 'B' and (resid 203 through 214 )BB203 - 214166 - 177

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