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- PDB-2jjw: Structure of human signal regulatory protein (sirp) gamma -

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Basic information

Entry
Database: PDB / ID: 2jjw
TitleStructure of human signal regulatory protein (sirp) gamma
ComponentsSIGNAL REGULATORY PROTEIN GAMMA
KeywordsCELL ADHESION / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN SUPERFAMILY / SIRP / SIRPG / MEMBRANE / GLYCOPROTEIN / SIGNAL REGULATORY PROTEIN GAMMA / TRANSMEMBRANE / PAIRED RECEPTOR / ALTERNATIVE SPLICING
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / Signal regulatory protein family interactions / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cell-cell signaling / cell adhesion / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation ...positive regulation of cell-cell adhesion / Signal regulatory protein family interactions / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cell-cell signaling / cell adhesion / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Signal-regulatory protein gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
CitationJournal: Mol.Cell / Year: 2008
Title: Paired Receptor Specificity Explained by Structures of Signal Regulatory Proteins Alone and Complexed with Cd47.
Authors: Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
History
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL REGULATORY PROTEIN GAMMA


Theoretical massNumber of molelcules
Total (without water)14,2131
Polymers14,2131
Non-polymers00
Water1,33374
1
A: SIGNAL REGULATORY PROTEIN GAMMA

A: SIGNAL REGULATORY PROTEIN GAMMA


Theoretical massNumber of molelcules
Total (without water)28,4272
Polymers28,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area1610 Å2
ΔGint-12.5 kcal/mol
Surface area13400 Å2
MethodPQS
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.390, 76.390, 78.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Antibody SIGNAL REGULATORY PROTEIN GAMMA / SIRP GAMMA / SIGNAL-REGULATORY PROTEIN BETA-2 / SIRP-BETA-2 / SIRP-B2 / CD172G ANTIGEN


Mass: 14213.292 Da / Num. of mol.: 1 / Fragment: N-TERMINAL ECTODOMAIN, RESIDUES 29-147
Source method: isolated from a genetically manipulated source
Details: ISOFORM 4 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q9P1W8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N- TERMINAL 28 AMINO ACID SIGNAL SEQUENCE). C- ...RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N- TERMINAL 28 AMINO ACID SIGNAL SEQUENCE). C-TERMINAL PURIFICATION TAG (TRHHHHHH) IS ADDED.

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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: 2.32 Å3/Da / Density % sol: 47.1 % / Description: NONE
Crystal growpH: 6.5
Details: 300 NL 11.5 MG/ML SIRP GAMMA PLUS 50 NL RESERVOIR (2.0 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PH 6.5) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 20.5 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→38.2 Å / Num. obs: 14652 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 32.3 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 43.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 33.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UV3 CHAIN A

2uv3


Resolution: 1.7→38.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.453 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 724 4.9 %RANDOM
Rwork0.228 ---
obs0.23 13927 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 74 925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022887
X-RAY DIFFRACTIONr_bond_other_d0.0030.02608
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9791210
X-RAY DIFFRACTIONr_angle_other_deg0.8343.0041492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86423.43832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30815152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.296155
X-RAY DIFFRACTIONr_chiral_restr0.0710.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_nbd_refined0.1980.2128
X-RAY DIFFRACTIONr_nbd_other0.20.2582
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2410
X-RAY DIFFRACTIONr_nbtor_other0.0840.2501
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2262598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8363916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9044355
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6866291
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 49
Rwork0.283 1058
Refinement TLS params.Method: refined / Origin x: 27.0388 Å / Origin y: 16.1268 Å / Origin z: 7.847 Å
111213212223313233
T-0.0513 Å20.0615 Å2-0.0345 Å2--0.2283 Å2-0.0223 Å2---0.2096 Å2
L5.4503 °2-1.041 °2-0.3249 °2-7.7766 °2-0.0085 °2--2.8087 °2
S-0.013 Å °-0.1028 Å °-0.238 Å °-0.691 Å °-0.163 Å °0.6712 Å °0.4727 Å °0.2582 Å °0.176 Å °

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