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- PDB-2jju: Structure of human signal regulatory protein (sirp) beta -

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Basic information

Entry
Database: PDB / ID: 2jju
TitleStructure of human signal regulatory protein (sirp) beta
ComponentsSIGNAL REGULATORY PROTEIN BETA-1
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN SUPERFAMILY / SIGNAL REGULATORY PROTEIN BETA / TRANSMEMBRANE / PAIRED RECEPTOR / ALTERNATIVE SPLICING / SIRP / SIRPB1 / MEMBRANE / POLYMORPHISM / GLYCOPROTEIN
Function / homology
Function and homology information


Signal regulatory protein family interactions / positive regulation of phagocytosis / secretory granule membrane / DAP12 interactions / positive regulation of T cell activation / cell surface receptor signaling pathway / Neutrophil degranulation / cell surface / signal transduction / plasma membrane
Similarity search - Function
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 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Signal-regulatory protein beta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
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 BETA-1
B: SIGNAL REGULATORY PROTEIN BETA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1625
Polymers27,9952
Non-polymers1673
Water6,179343
1
A: SIGNAL REGULATORY PROTEIN BETA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1293
Polymers13,9981
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGNAL REGULATORY PROTEIN BETA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers13,9981
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.166, 65.172, 58.113
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody SIGNAL REGULATORY PROTEIN BETA-1 / SIRP-BETA-1 / CD172B ANTIGEN / SIRP BETA


Mass: 13997.745 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ECTODOMAIN, RESIDUES 30-148
Source method: isolated from a genetically manipulated source
Details: 2 ISOFORMS PRODUCED BY ALTERNATIVE SPLICING. IN THIS ENTRY ISOFORM 1 (O00241-1) IS PRESENT
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: O00241
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N- TERMINAL 29 AMINO ACID SIGNAL SEQUENCE). C- ...RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N- TERMINAL 29 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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 7
Details: 400 NL 25 MG/ML SIRP BETA PLUS 50 NL RESERVOIR (2.5 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PROPANE PH 7.0) 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: 0.958
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 7, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 76112 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UV3, CHAIN A

2uv3


Resolution: 1.19→32.11 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 3809 5 %RANDOM
Rwork0.139 ---
obs0.14 72274 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0.18 Å2
2--0.01 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.19→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 7 343 2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221801
X-RAY DIFFRACTIONr_bond_other_d0.0020.021266
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9692456
X-RAY DIFFRACTIONr_angle_other_deg0.7483.0033096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00123.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1571515
X-RAY DIFFRACTIONr_chiral_restr0.0740.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_nbd_refined0.1750.2249
X-RAY DIFFRACTIONr_nbd_other0.2020.21320
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2844
X-RAY DIFFRACTIONr_nbtor_other0.0830.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.88721478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.45631843
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4544771
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5746598
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: 1.19→1.22 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.215 247
Rwork0.186 5238

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