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

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Basic information

Entry
Database: PDB / ID: 2jjv
TitleStructure of human signal regulatory protein (sirp) beta(2)
ComponentsSIGNAL-REGULATORY PROTEIN BETA 1.
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / SIGNAL REGULATORY PROTEIN BETA / SIRP / SIRPB2 / PAIRED RECEPTOR
Function / homology
Function and homology information


: / 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 beta-1 isoform 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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)28,6417
Polymers28,2222
Non-polymers4205
Water2,504139
1
A: SIGNAL-REGULATORY PROTEIN BETA 1.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2072
Polymers14,1111
Non-polymers961
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)14,4345
Polymers14,1111
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.979, 47.490, 40.044
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody SIGNAL-REGULATORY PROTEIN BETA 1. / SIRP BETA 2


Mass: 14110.844 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: Q5TFQ8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 1.94 Å3/Da / Density % sol: 36.5 % / Description: NONE
Crystal growpH: 6
Details: 300 NL 25 MG/ML SIRP BETA PLUS 100 NL RESERVOIR (3.2 M AMMONIUM SULPHATE, 0.1 M MES PH 6.0) 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: 0.979
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19509 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.4 / % possible all: 79.1

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Processing

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

2uv3


Resolution: 1.8→57.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.741 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1002 5.1 %RANDOM
Rwork0.172 ---
obs0.174 18506 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20.02 Å2
2---0.35 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 21 139 1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221833
X-RAY DIFFRACTIONr_bond_other_d0.0010.021231
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9632511
X-RAY DIFFRACTIONr_angle_other_deg0.7523.0043006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9462370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16515291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5091513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined0.1840.2264
X-RAY DIFFRACTIONr_nbd_other0.1980.21259
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2837
X-RAY DIFFRACTIONr_nbtor_other0.080.21012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23821244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65231912
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6044711
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9326594
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 61
Rwork0.175 1074
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.50320.34871.86712.1864-0.10242.18790.1611-0.0673-0.2754-0.36560.12510.40790.2111-0.2244-0.28620.0582-0.0379-0.1065-0.00630.03490.03167.19634.2077.537
24.3411-1.30692.02886.9772.56617.6564-0.0047-0.8886-0.69880.20990.01690.51990.779-0.8476-0.0123-0.0383-0.13740.03080.1830.07580.0193-1.17435.53115.398
34.12260.73240.61094.4159-0.67242.45880.1708-0.3715-0.3301-0.24040.09670.43030.2365-0.2017-0.26750.0285-0.057-0.1140.05720.06530.04346.02434.53510.834
44.0097-1.2941.304617.5473-5.22275.95530.0629-0.0099-0.2626-0.59490.2540.26510.2819-0.0292-0.3168-0.0316-0.0178-0.10680.0513-0.02040.024711.2433.7837.707
51.21220.5412-0.89031.4599-0.80492.0475-0.0620.12920.0784-0.13940.05260.03350.0778-0.13540.00950.1024-0.0069-0.00610.0288-0.0020.003922.25949.43611.906
62.21961.09990.16415.08090.77943.42420.04760.002-0.0699-0.047-0.0428-0.42050.25940.1062-0.00470.04260.02890.0057-0.0020.01330.028633.91147.53715.453
70.4869-0.2708-0.02281.3305-0.18180.83270.02010.0627-0.018-0.043-0.0849-0.10790.03680.02840.06480.07950.0050.00870.01930.003-0.009625.79339.74214.276
81.61980.3793-0.90862.2337-1.26995.4511-0.01-0.00850.0152-0.0435-0.0234-0.19210.10440.24890.03340.1001-0.0024-0.0090.0190.0060.054630.36951.78114.346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION2A51 - 68
3X-RAY DIFFRACTION3A69 - 99
4X-RAY DIFFRACTION4A100 - 115
5X-RAY DIFFRACTION5B2 - 35
6X-RAY DIFFRACTION6B36 - 54
7X-RAY DIFFRACTION7B55 - 84
8X-RAY DIFFRACTION8B85 - 116

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