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- PDB-6mvl: Crystal structure of VISTA bound to a pH-selective antibody Fab f... -

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Basic information

Entry
Database: PDB / ID: 6mvl
TitleCrystal structure of VISTA bound to a pH-selective antibody Fab fragment
Components
  • (Antibody Fab fragment ...) x 2
  • V-type immunoglobulin domain-containing suppressor of T-cell activation
KeywordsIMMUNE SYSTEM / immunoglobulin / checkpoint / antibody / complex
Function / homology
Function and homology information


positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production ...positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / endopeptidase activator activity / regulation of immune response / positive regulation of cell migration / positive regulation of gene expression / enzyme binding / identical protein binding / plasma membrane
Similarity search - Function
V-type immunoglobulin domain-containing suppressor of T-cell activation / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...V-type immunoglobulin domain-containing suppressor of T-cell activation / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
V-type immunoglobulin domain-containing suppressor of T-cell activation
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsCritton, D.A.
CitationJournal: Nature / Year: 2019
Title: VISTA is an acidic pH-selective ligand for PSGL-1.
Authors: Johnston, R.J. / Su, L.J. / Pinckney, J. / Critton, D. / Boyer, E. / Krishnakumar, A. / Corbett, M. / Rankin, A.L. / Dibella, R. / Campbell, L. / Martin, G.H. / Lemar, H. / Cayton, T. / ...Authors: Johnston, R.J. / Su, L.J. / Pinckney, J. / Critton, D. / Boyer, E. / Krishnakumar, A. / Corbett, M. / Rankin, A.L. / Dibella, R. / Campbell, L. / Martin, G.H. / Lemar, H. / Cayton, T. / Huang, R.Y. / Deng, X. / Nayeem, A. / Chen, H. / Ergel, B. / Rizzo, J.M. / Yamniuk, A.P. / Dutta, S. / Ngo, J. / Shorts, A.O. / Ramakrishnan, R. / Kozhich, A. / Holloway, J. / Fang, H. / Wang, Y.K. / Yang, Z. / Thiam, K. / Rakestraw, G. / Rajpal, A. / Sheppard, P. / Quigley, M. / Bahjat, K.S. / Korman, A.J.
History
DepositionOct 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type immunoglobulin domain-containing suppressor of T-cell activation
H: Antibody Fab fragment heavy chain
L: Antibody Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40418
Polymers66,8383
Non-polymers1,56615
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-187 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.166, 125.856, 192.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11H-522-

HOH

21L-678-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Antibody Fab fragment heavy chain


Mass: 24371.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody Fab fragment light chain


Mass: 23362.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein V-type immunoglobulin domain-containing suppressor of T-cell activation / Platelet receptor Gi24 / Stress-induced secreted protein-1 / Sisp-1 / V-set domain-containing ...Platelet receptor Gi24 / Stress-induced secreted protein-1 / Sisp-1 / V-set domain-containing immunoregulatory receptor / V-set immunoregulatory receptor


Mass: 19104.275 Da / Num. of mol.: 1 / Mutation: N91Q, N108Q, N190Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIR, C10orf54, SISP1, VISTA, PP2135, UNQ730/PRO1412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7M9
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 772 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.8 M ammonium sulfate, 0.1 M phosphate/citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2018 / Details: Kirkpatrick-Baez
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.606→96.02 Å / Num. obs: 55883 / % possible obs: 88.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.39 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.8
Reflection shellResolution: 1.606→1.807 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2795 / % possible all: 73.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→96.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2759 4.94 %RANDOM
Rwork0.182 ---
obs0.184 55883 53.4 %-
Displacement parametersBiso mean: 34.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.233 Å20 Å20 Å2
2--2.7401 Å20 Å2
3----0.5071 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.61→96.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 84 758 5120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084470HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.076101HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1453SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes746HARMONIC5
X-RAY DIFFRACTIONt_it4470HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion17.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion584SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5556SEMIHARMONIC4
LS refinement shellResolution: 1.61→1.73 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2506 -4.92 %
Rwork0.2439 1063 -
all0.2443 1118 -
obs--5.58 %
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)
16.53612.68490.52792.9625-0.40212.6367-0.17210.9110.0292-0.15830.2880.09310.0839-0.3836-0.1159-0.097-0.0302-0.02120.32740.0677-0.1434-38.311314.267412.7294
21.26620.285-0.19590.74190.0910.2908-0.00310.08950.1388-0.03510.00480.0155-0.0489-0.041-0.0017-0.06710.0159-0.0169-0.03950.0303-0.0585-5.752517.544639.5212
31.880.36530.4750.93010.01290.5298-0.05150.17820.0571-0.01590.0385-0.15370.0561-0.02560.0131-0.0841-0.0026-0.0009-0.0453-0.0051-0.05326.72875.095634.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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