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- PDB-6lpg: human VASH1-SVBP complex -

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Basic information

Entry
Database: PDB / ID: 6lpg
Titlehuman VASH1-SVBP complex
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsHYDROLASE / TUBULIN CARBOXYPEPTIDASES / MICROTUBULE MODIFICATION / ANGIOGENESIS
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / negative regulation of lymphangiogenesis / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / peptidase activator activity / axon development / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / negative regulation of angiogenesis / response to wounding / apical part of cell / actin binding / angiogenesis / microtubule binding / cytoskeleton / regulation of cell cycle / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23
Similarity search - Domain/homology
Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIkeda, A. / Nishino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07279 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: The crystal structure of the tetrameric human vasohibin-1-SVBP complex reveals a variable arm region within the structural core.
Authors: Ikeda, A. / Urata, S. / Ando, T. / Suzuki, Y. / Sato, Y. / Nishino, T.
History
DepositionJan 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulinyl-Tyr carboxypeptidase 1
B: Small vasohibin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5266
Polymers37,1422
Non-polymers3844
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-62 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.854, 71.854, 215.811
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Tubulinyl-Tyr carboxypeptidase 1 / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


Mass: 29336.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase
#2: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 7804.847 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8N300
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.16 M ammonium sulfate, 0.08 M Sodium acetate pH4.6, 20%(w/v) PEG4000, 20%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.06 Å / Num. obs: 15488 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 48.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01637 / Rpim(I) all: 0.01637 / Rrim(I) all: 0.02315 / Net I/σ(I): 24.05
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.2435 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 1492 / CC1/2: 0.86 / Rpim(I) all: 0.2435 / Rrim(I) all: 0.3443

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVQ

6nvq


Resolution: 2.3→47.06 Å / SU ML: 0.2662 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 1548 10 %
Rwork0.1896 13926 -
obs0.1942 15474 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 20 76 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682332
X-RAY DIFFRACTIONf_angle_d0.85133148
X-RAY DIFFRACTIONf_chiral_restr0.0494332
X-RAY DIFFRACTIONf_plane_restr0.0047405
X-RAY DIFFRACTIONf_dihedral_angle_d17.5708893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.30291360.23231224X-RAY DIFFRACTION100
2.37-2.460.27321350.21751217X-RAY DIFFRACTION100
2.46-2.560.26061380.21441244X-RAY DIFFRACTION100
2.56-2.670.26081380.20561233X-RAY DIFFRACTION100
2.67-2.810.27791370.18251237X-RAY DIFFRACTION100
2.81-2.990.25521400.18371259X-RAY DIFFRACTION100
2.99-3.220.20061380.17961238X-RAY DIFFRACTION100
3.22-3.550.2141400.17671272X-RAY DIFFRACTION100
3.55-4.060.20981430.16191280X-RAY DIFFRACTION99.93
4.06-5.110.20711440.17811300X-RAY DIFFRACTION99.31
5.11-100.27421590.22091422X-RAY DIFFRACTION99.81
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)
11.434331741960.936701917329-0.1526607516514.516032774660.7555283940111.6750399867-0.1856843481790.2445151510880.5859877867880.153772604204-0.02847558880251.04116382184-0.149825900202-0.0573973716810.1025483718560.420090550240.0185267628962-0.07856548827760.4545072017040.06575170922140.869369066589-7.6644036807815.4664254304-16.0546774521
22.410564807211.92122806188-0.9018429062812.683785995-0.9469949941932.634307791850.01532247260430.719727577723-0.00874178708856-0.5563620730360.1567926928130.103304285182-0.5375894932060.0494584470052-0.1665158402560.543175504773-0.0889519932075-0.07849072263460.4178762592820.003606612052590.359926990219.967078492117.3466902801-26.2399401664
34.08146818848-0.151976618004-0.0163121886273.336185659750.1658994801680.785291859731-0.295754217261-0.078743025094-0.09846123663140.1862068191590.1584970434570.6413103273060.11770778837-0.305193140939-0.01209339167660.458025487268-0.0738706633968-0.005317927387820.353802589648-0.01162455623420.42867451530210.2507262298.98657560876-15.6176499199
42.76341834267-0.347371141134-0.4684077920291.77644878539-0.3824095223185.98725738772-0.173846422255-0.2000899677530.2235530982130.2583967891710.249630366761-0.102155662356-0.18596769820.0917560944692-0.02672506805440.348401465604-0.009621778433050.02485057325420.23902685183-0.05731525055850.26050275035721.786298307513.885954083-7.28901589608
52.75695436811-1.40332251482-2.354856012174.435245945151.026770939194.65482822139-0.157599935464-0.2942479880971.311407913460.452334252160.3485448028570.247602591854-0.365699043734-0.1124479890440.04626292192390.4861686659470.0244470394143-0.01286087969490.329523752461-0.07708110710420.46194603881622.729297100220.5687923046-11.4995178295
65.79428974663-0.5451124382720.5439014797113.688304430760.4999350929667.03010108657-0.0172429759959-0.1611257297580.6349645623430.669931706382-0.130329113848-0.342372779004-0.5049160746960.397673585020.1310334481310.529957768155-0.057428032191-0.02207300481820.226604455639-0.03268192667130.31001724739527.693576517222.1270908996-7.22738821467
72.5658754435-0.301161448917-0.2719572159577.259785426376.784148799219.8770241427-0.0228922344116-0.127812639862-0.1253255439530.4234269928680.661523775346-0.3113310892540.4088006860350.584247314836-0.6417046952280.4804472561190.04820832114730.06330506447570.296890066550.05851237674040.36844744580922.89308033639.69987215384-6.64385607291
85.249062272762.361797030364.055055294826.104635600155.211120755398.36577284292-0.140440157644-0.982748426893-0.2204941248920.9549485600370.0826989346045-0.05289384082310.9566844348790.330014110420.0509472523110.674899295346-0.006285463438380.006333079998980.6874233133650.0560336191580.37054279143725.72706957767.423661867040.158684841206
98.75414065319-2.68051876913-2.175910515583.487320301133.443735712623.43151888722-0.433228638294-0.17897662173-0.325201930507-0.577028306911-0.439870461159-0.5876761920540.4435210804621.429893371290.4687246220490.9166449336150.153878599552-0.05255748224371.048855084810.2806577362750.89533718569636.34882860749.92678910672-2.49913259963
104.208522862862.439222792890.2143179272178.572653941484.264397097296.25290160033-0.2109564037390.5574344247650.257638178453-0.3770834284460.3402613271690.548505042519-0.3764787257520.249724268649-0.08523849198920.4475861997330.0618971087951-0.1303563995320.411616565180.1439819491570.826518145338-2.1626458744420.8486438021-18.3691465872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 226 )
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 250 )
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 269 )
8X-RAY DIFFRACTION8chain 'A' and (resid 270 through 287 )
9X-RAY DIFFRACTION9chain 'A' and (resid 288 through 304 )
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 53 )

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