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- PDB-8tbq: The crystal structure of human VISTA extra cellular domain in com... -

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Basic information

Entry
Database: PDB / ID: 8tbq
TitleThe crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody
Components
  • SNS-101 Fab heavy chain
  • SNS-101 Fab light chain
  • V-type immunoglobulin domain-containing suppressor of T-cell activation
KeywordsPROTEIN BINDING / IMMUNE SYSTEM / VISTA / pH-selective / SNS-101 / PD-1
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 / Immunoglobulin-like fold
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: 2.593 Å
Authorsvan der Horst, E.H. / Mukherjee, A. / Thisted, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The pH-selective anti-VISTA antibody SNS-101 displays a favorable pharmacokinetic and safety profile and promotes anti-tumoral M1 macrophage polarization in PD-1 refractory settings
Authors: Thisted, T. / Smith, F.D. / Zhang, G. / Feng, F. / Kleschenko, Y. / Mukherjee, A. / Jiang, Z. / Malhotra, K. / Biesova, Z. / Onumajuru, A. / Gaelle, M. / Takeuchi, Y. / Thiam, K. / ...Authors: Thisted, T. / Smith, F.D. / Zhang, G. / Feng, F. / Kleschenko, Y. / Mukherjee, A. / Jiang, Z. / Malhotra, K. / Biesova, Z. / Onumajuru, A. / Gaelle, M. / Takeuchi, Y. / Thiam, K. / Schreiber, R.D. / van der Horst, E.H.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: SNS-101 Fab heavy chain
L: SNS-101 Fab light chain
P: V-type immunoglobulin domain-containing suppressor of T-cell activation
A: SNS-101 Fab heavy chain
B: SNS-101 Fab light chain
Q: V-type immunoglobulin domain-containing suppressor of T-cell activation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,21211
Polymers131,4246
Non-polymers7885
Water84747
1
H: SNS-101 Fab heavy chain
L: SNS-101 Fab light chain
P: V-type immunoglobulin domain-containing suppressor of T-cell activation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0576
Polymers65,7123
Non-polymers3453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SNS-101 Fab heavy chain
B: SNS-101 Fab light chain
Q: V-type immunoglobulin domain-containing suppressor of T-cell activation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1545
Polymers65,7123
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.659, 39.512, 177.979
Angle α, β, γ (deg.)90.000, 117.121, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21H
32H
42H
53H
63H

NCS domain segments:

Auth asym-ID: H / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYS1 - 2231 - 223
211GLUGLULYSLYS1 - 2231 - 223
322GLUGLUASNASN1 - 2081 - 208
422GLUGLUASNASN1 - 2081 - 208
533SERSERLEULEU33 - 18433 - 184
633SERSERLEULEU33 - 18433 - 184

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody SNS-101 Fab heavy chain


Mass: 24336.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: CHO / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody SNS-101 Fab light chain


Mass: 23414.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 5 molecules PQ

#3: Protein V-type immunoglobulin domain-containing suppressor of T-cell activation


Mass: 17961.055 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9H7M9
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 49 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M BIS-TRIS propane, 0.2 M NaBr, 22%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.593→158.409 Å / Num. obs: 26185 / % possible obs: 84.6 % / Redundancy: 4.27 % / CC1/2: 0.996 / Net I/σ(I): 8.9
Reflection shellResolution: 2.593→2.837 Å / Redundancy: 4.58 % / Num. unique obs: 1309 / CC1/2: 0.695 / % possible all: 52.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.593→158.409 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.854 / SU B: 14.502 / SU ML: 0.306 / Cross valid method: FREE R-VALUE / ESU R Free: 0.522
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.291 1291 4.93 %
Rwork0.2366 24894 -
all0.239 --
obs-26185 63.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.294 Å20 Å2-0.481 Å2
2---0.97 Å20 Å2
3---0.766 Å2
Refinement stepCycle: LAST / Resolution: 2.593→158.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8440 0 50 47 8537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0128717
X-RAY DIFFRACTIONr_bond_other_d0.0260.0167528
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.65211897
X-RAY DIFFRACTIONr_angle_other_deg0.5771.55817496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22751127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.639542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86101201
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.99910350
X-RAY DIFFRACTIONr_chiral_restr0.0440.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021734
X-RAY DIFFRACTIONr_nbd_refined0.1450.21342
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1550.27059
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24157
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.223
X-RAY DIFFRACTIONr_nbd_other0.1070.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0880.22
X-RAY DIFFRACTIONr_mcbond_it1.95.7714535
X-RAY DIFFRACTIONr_mcbond_other1.95.7714535
X-RAY DIFFRACTIONr_mcangle_it3.358.6425653
X-RAY DIFFRACTIONr_mcangle_other3.358.6425654
X-RAY DIFFRACTIONr_scbond_it1.3325.4974182
X-RAY DIFFRACTIONr_scbond_other1.3325.4974183
X-RAY DIFFRACTIONr_scangle_it2.4018.2886244
X-RAY DIFFRACTIONr_scangle_other2.4018.2886245
X-RAY DIFFRACTIONr_lrange_it5.20568.4688823
X-RAY DIFFRACTIONr_lrange_other5.20268.4748820
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.052219
X-RAY DIFFRACTIONr_ncsr_local_group_20.0410.051857
X-RAY DIFFRACTIONr_ncsr_local_group_30.0610.051564
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11HX-RAY DIFFRACTIONLocal ncs0.045250.05
12HX-RAY DIFFRACTIONLocal ncs0.045250.05
23HX-RAY DIFFRACTIONLocal ncs0.041140.05
24HX-RAY DIFFRACTIONLocal ncs0.041140.05
35HX-RAY DIFFRACTIONLocal ncs0.061240.05
36HX-RAY DIFFRACTIONLocal ncs0.061240.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.593-2.660.39680.3521530.35430070.9250.8965.35420.353
2.66-2.7330.442270.363500.36528620.8490.92713.17260.36
2.733-2.8120.319320.2765410.27928930.9280.95219.80640.268
2.812-2.8990.336370.2977160.29927110.9360.94127.77570.284
2.899-2.9940.295680.28210000.28227070.9280.94839.45330.262
2.994-3.0990.316840.2913330.29225840.9290.94454.83750.264
3.099-3.2160.299670.27816470.27925070.9390.94768.36860.258
3.216-3.3470.321950.27718470.27924000.9330.94880.91670.252
3.347-3.4960.3121010.25819730.26123160.9420.95589.55090.227
3.496-3.6660.308910.26720060.26922100.9330.95294.88690.235
3.666-3.8650.316970.25217910.25521150.9350.95889.26710.225
3.865-4.0990.284660.21214120.21519980.9490.97273.9740.197
4.099-4.3820.226820.19818460.19919280.970.9751000.181
4.382-4.7320.226940.17616410.17817350.9710.9811000.169
4.732-5.1840.223720.1915590.19116320.9740.97799.93870.184
5.184-5.7950.31830.22814050.23214900.9580.96899.86580.218
5.795-6.690.306710.25512450.25813230.9360.95899.47090.246
6.69-8.1890.366630.25610640.26111330.9290.95899.47040.258
8.189-11.5660.336330.2138510.2178870.9290.9799.66180.233
11.566-158.4090.373200.3355130.3365390.90.89498.88680.436

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