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- PDB-4gos: Crystal structure of human B7-H4 IgV-like domain -

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Basic information

Entry
Database: PDB / ID: 4gos
TitleCrystal structure of human B7-H4 IgV-like domain
ComponentsV-set domain-containing T-cell activation inhibitor 1
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN / DISULFIDE BOND / IMMUNITY / ADAPTIVE IMMUNITY / Structural Genomics / PSI-Biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / IMMUNOGLOBULIN VARIABLE-LIKE DOMAIN / CELL SURFACE / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


interleukin-4 production / response to protozoan / type II interferon production / negative regulation of T cell activation / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / regulation of cytokine production / positive regulation of interleukin-2 production / T cell receptor signaling pathway ...interleukin-4 production / response to protozoan / type II interferon production / negative regulation of T cell activation / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / regulation of cytokine production / positive regulation of interleukin-2 production / T cell receptor signaling pathway / adaptive immune response / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process
Similarity search - Function
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 ...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-set domain-containing T-cell activation inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.59 Å
AuthorsVigdorovich, V. / Ramagopal, U. / Bhosle, R. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Cell Rep / Year: 2014
Title: Structure and cancer immunotherapy of the B7 family member B7x.
Authors: Jeon, H. / Vigdorovich, V. / Garrett-Thomson, S.C. / Janakiram, M. / Ramagopal, U.A. / Abadi, Y.M. / Lee, J.S. / Scandiuzzi, L. / Ohaegbulam, K.C. / Chinai, J.M. / Zhao, R. / Yao, Y. / Mao, ...Authors: Jeon, H. / Vigdorovich, V. / Garrett-Thomson, S.C. / Janakiram, M. / Ramagopal, U.A. / Abadi, Y.M. / Lee, J.S. / Scandiuzzi, L. / Ohaegbulam, K.C. / Chinai, J.M. / Zhao, R. / Yao, Y. / Mao, Y. / Sparano, J.A. / Almo, S.C. / Zang, X.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-set domain-containing T-cell activation inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6332
Polymers13,7221
Non-polymers9111
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.500, 46.500, 115.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

Detailsprobable monomer

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Components

#1: Protein V-set domain-containing T-cell activation inhibitor 1 / B7h.5 / Immune costimulatory protein B7-H4 / Protein B7S1 / T-cell costimulatory molecule B7x


Mass: 13722.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B7-H4, B7H4, B7S1, B7x, UNQ659/PRO1291, VTCN1 / Plasmid: modified pMT-BiP-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 cell line / References: UniProt: Q7Z7D3
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2846.06
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion7200 mM tri-Potassium citrate, 2.2 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, temperature 291K
2912vapor diffusion7200 mM tri-Potassium citrate, 2.2 M ammonium sulfate, I3C (magic triangle) soak, pH 7.0, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0750, 1.5402
NSLS X29A2
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
21.54021
ReflectionRedundancy: 18.4 % / Av σ(I) over netI: 4.3 / Number: 201521 / Rsym value: 0.161 / D res high: 1.793 Å / D res low: 43.145 Å / Num. obs: 10948 / % possible obs: 86.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6738.7299.610.0690.06918.8
4.015.6710010.0620.06220.5
3.274.0175.310.0840.08417.4
2.843.2710010.0990.09917.1
2.542.8486.810.1520.15217.1
2.312.5499.610.2080.20817.3
2.142.318310.4080.40817.8
22.1483.110.4720.47218.9
1.89266.711.0161.01619.6
1.791.8989.411.7921.79219.7
ReflectionResolution: 1.59→43.149 Å / Num. all: 17917 / Num. obs: 16143 / % possible obs: 90.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 13.046 Å2 / Rsym value: 0.088 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.59-1.6813.51.63452525480.489100
1.68-1.7814.12.43051721590.31589.6
1.78-1.913.93.82923521090.19893
1.9-2.0513.45.32264816870.12878.8
2.05-2.2513.16.12118216160.11381.9
2.25-2.5212.87.62147916740.08892.9
2.52-2.912.58.51808914490.07389.9
2.9-3.5612.28.71574312860.0793.5
3.56-5.0312.711.3119809420.05385.5
5.03-38.5912.713.985556730.04298.9

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Phasing

PhasingMethod: SIRAS
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
130.99223.73710.724S201
233.25124.08716.194S200.58
328.32727.52514.529S200.34
430.69543.65917.143S200.16
528.03321.9111.079S200.15
630.50818.5042.543S200.14
733.44545.94915.446S200.1
832.36922.2565.436S200.08
932.41823.80323.98S200.08
1028.91145.26111.786S200.06
1137.86654.3368.5S200.02

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.59→19.91 Å / WRfactor Rfree: 0.1935 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9077 / SU B: 1.216 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0905 / SU Rfree: 0.0847 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES HAVE BEEN REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 837 5.2 %RANDOM
Rwork0.1741 ---
obs0.175 15194 89.82 %-
all-16916 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 46.49 Å2 / Biso mean: 15.8718 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.59→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 61 111 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02960
X-RAY DIFFRACTIONr_bond_other_d0.0020.02917
X-RAY DIFFRACTIONr_angle_refined_deg1.4742.0451307
X-RAY DIFFRACTIONr_angle_other_deg0.7253.0022102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73725.94637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60915164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.761153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02188
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 68 -
Rwork0.232 1198 -
all-1266 -
obs-1198 99.29 %

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