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- PDB-7n1o: The von Willebrand factor A domain of human capillary morphogenes... -

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Basic information

Entry
Database: PDB / ID: 7n1o
TitleThe von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone
ComponentsTranscription factor ETV6,Isoform 4 of Anthrax toxin receptor 2
KeywordsPROTEIN BINDING / von Willebrand factor type A domain / Collagen binding / alpha-beta / MIDAS
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / collagen fibril organization / hematopoietic stem cell proliferation / uterus development / Uptake and function of anthrax toxins / single fertilization / neurogenesis / Signaling by FLT3 fusion proteins ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / collagen fibril organization / hematopoietic stem cell proliferation / uterus development / Uptake and function of anthrax toxins / single fertilization / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane signaling receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / endosome membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / external side of plasma membrane / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / chromatin / nucleolus / cell surface / negative regulation of transcription by RNA polymerase II / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
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 / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 ...Anthrax toxin receptor / Anthrax toxin receptor, C-terminal / Anthrax toxin receptor, extracellular domain / Anthrax receptor C-terminus region / Anthrax receptor extracellular domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / Sterile alpha motif/pointed domain superfamily / von Willebrand factor A-like domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription factor ETV6 / Anthrax toxin receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsMathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Sarath Nawarathnage, S.D. / Doukov, T. / Moody, J.D.
CitationJournal: Open Biology / Year: 2022
Title: Crystals of TELSAM-target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts.
Authors: Nawarathnage, S. / Soleimani, S. / Mathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Gajjar, P. / Bunn, D.R. / Stewart, C. / Smith, T. / Pedroza Romo, M.J. / Brown, S. / Doukov, T. / Moody, J.D.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Mar 9, 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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,Isoform 4 of Anthrax toxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7434
Polymers28,6481
Non-polymers953
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Previously-observed in PDB structures of this protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-32 kcal/mol
Surface area11420 Å2
Unit cell
Length a, b, c (Å)103.396, 103.396, 56.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Transcription factor ETV6,Isoform 4 of Anthrax toxin receptor 2 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / Capillary morphogenesis gene 2 protein / CMG-2


Mass: 28647.684 Da / Num. of mol.: 1
Mutation: 1TEL: R41A,D46G,V112E,K122A,vWa: R49A,C175A,V112A,K112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P58335
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 8 / 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: 3.04 Å3/Da / Density % sol: 59.59 % / Description: rod-like hexagonal prism
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 100 mM BisTris, 3.0 M NaCl

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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 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.77→38.16 Å / Num. obs: 8679 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 71.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05193 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05753 / Net I/σ(I): 18.35
Reflection shellResolution: 2.77→2.869 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.6253 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 878 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.2779 / Rrim(I) all: 0.6876 / % possible all: 97.99

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9model building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QB1, 1SHU

2qb1

1shu


Resolution: 2.77→38.16 Å / SU ML: 0.3932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 434 4.99 %
Rwork0.2033 8256 -
obs0.2045 8679 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.23 Å2
Refinement stepCycle: LAST / Resolution: 2.77→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 3 8 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851960
X-RAY DIFFRACTIONf_angle_d0.85622667
X-RAY DIFFRACTIONf_chiral_restr0.0484309
X-RAY DIFFRACTIONf_plane_restr0.0066343
X-RAY DIFFRACTIONf_dihedral_angle_d12.9234682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-3.170.361540.31242716X-RAY DIFFRACTION97.45
3.17-3.990.27131280.22592780X-RAY DIFFRACTION97.95
3.99-38.160.18191520.16932760X-RAY DIFFRACTION96.14
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)
17.68107769229-2.662601585540.8195439767885.4168714507-0.8615700999024.14197555455-0.0243071327921-0.5480682219320.7067447481190.3800355638520.0209146150898-0.211689604287-0.6447607492790.1229879002190.04622659762320.572192442917-0.0878142654727-0.02568803328670.436825793903-0.067677996540.36034857982210.694543034818.564193244922.6213169989
23.719015919743.56378363838-4.230304210644.96749592295-5.061549655488.00674075391-0.01770282693630.1321631274250.05709102810080.4837083073220.0356145517246-0.469918777609-0.6539580991380.1603530105730.01595600063160.4714484312550.0441558551384-0.05499197356930.435681556624-0.007878141601430.50239766911520.400582335229.73137964055.5724152921
35.67455665372-1.412654275370.4279830414925.48219750154-0.6813082764057.77376452635-0.3420459190320.3461801385040.0862840489978-0.449760901534-0.171738294562-0.9268665788280.1276214847260.6360507473880.3095686424280.517365608413-0.09735303858530.06677852429280.5258484599970.0008638971136010.52694166579131.172561330632.8494104899-2.73678281731
43.668658750151.17431420296-0.7364756531414.89539020493-5.367030339959.45250165017-0.1957203277180.5849513928880.243374388839-0.200513234220.7718908368480.420034114021-0.434437904443-0.798495500866-0.4576175508380.560502702403-0.089234218648-0.01295131653180.6158128686740.06428701977540.54666137989316.786160220135.2023056801-5.59741725619
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 1 through 64 )1 - 641 - 64
22chain 'A' and (resid 65 through 112 )65 - 11265 - 112
33chain 'A' and (resid 113 through 159 )113 - 159113 - 159
44chain 'A' and (resid 160 through 257 )160 - 257160 - 257

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