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- PDB-4i0k: Crystal structure of murine B7-H3 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 4i0k
TitleCrystal structure of murine B7-H3 extracellular domain
ComponentsCD276 antigen
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN / IMMUNITY / ADAPTIVE IMMUNITY / Structural Genomics / Protein Structure Initiative / immunoglobulin variable like domain / immunoglobulin constant like domain / cell surface / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


negative regulation of interleukin-2 production / negative regulation of type II interferon production / regulation of immune response / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / regulation of cytokine production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / T cell activation ...negative regulation of interleukin-2 production / negative regulation of type II interferon production / regulation of immune response / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / regulation of cytokine production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / T cell activation / negative regulation of inflammatory response / positive regulation of type II interferon production / T cell receptor signaling pathway / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding / identical protein binding
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.97 Å
AuthorsVigdorovich, V. / Ramagopal, U. / Bonanno, J.B. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Structure / Year: 2013
Title: Structure and T cell inhibition properties of B7 family member, B7-H3.
Authors: Vigdorovich, V. / Ramagopal, U.A. / Lazar-Molnar, E. / Sylvestre, E. / Lee, J.S. / Hofmeyer, K.A. / Zang, X. / Nathenson, S.G. / Almo, S.C.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: CD276 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4275
Polymers24,2651
Non-polymers1,1624
Water905
1
A: CD276 antigen
hetero molecules

A: CD276 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,85410
Polymers48,5302
Non-polymers2,3248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area7580 Å2
ΔGint-42 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 188.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, -x+y, -z-1/3

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Components

#1: Antibody CD276 antigen / B7 homolog 3 / B7-H3 / Costimulatory molecule


Mass: 24264.998 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B7-H3, B7h3, Cd276 / Plasmid: pMT-BiP-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 cell line / References: UniProt: Q8VE98
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 5.7 Å3/Da / Density % sol: 78.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES, pH 7.5; 20% PEG-10000, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9789
2
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 19, 2009
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si crystalSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.833→87.399 Å / Num. obs: 12250 / % possible obs: 99.7 % / Redundancy: 13.1 % / Rsym value: 0.117 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.97-3.1313.70.810.81,2100
3.13-3.3213.60.4421.70.4421,2100
3.32-3.5513.40.2772.70.2771,2100
3.55-3.8313.30.1814.20.1811,299.9
3.83-4.213.30.1116.60.1111,299.8
4.2-4.712.70.0867.80.0861,299.7
4.7-5.4211.90.0857.40.0851,299.6
5.42-6.6412.30.079.40.071,299.4
6.64-9.3913.20.04612.50.0461,299.2
9.39-48.73811.40.04114.90.0411,297.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BIS

3bis


Resolution: 2.97→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.178 / SU ML: 0.211 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24974 589 4.8 %RANDOM
Rwork0.21548 ---
obs0.21712 11661 99.5 %-
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 mean: 72.265 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 74 5 1592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191638
X-RAY DIFFRACTIONr_bond_other_d0.0020.021492
X-RAY DIFFRACTIONr_angle_refined_deg1.7422.0032246
X-RAY DIFFRACTIONr_angle_other_deg0.8413.0023415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.355201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73624.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.03415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.567159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 46 -
Rwork0.289 817 -
obs--100 %

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