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- PDB-9tf5: Structure of human wild-type signal regulatory protein alpha V2 v... -

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Basic information

Entry
Database: PDB / ID: 9tf5
TitleStructure of human wild-type signal regulatory protein alpha V2 variant (SIRPaV2) with zinc
ComponentsIsoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / Immunoglobulin superfamily / Signal regulatory protein alpha / paired receptor / SIRPalpha / SIRPa / SIRPaV2
Function / homology
Function and homology information


cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / GTPase regulator activity / cell-cell adhesion mediator activity / regulation of type II interferon production / negative regulation of lipopolysaccharide-mediated signaling pathway ...cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / GTPase regulator activity / cell-cell adhesion mediator activity / regulation of type II interferon production / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of nitric oxide biosynthetic process / regulation of tumor necrosis factor production / protein antigen binding / negative regulation of interferon-beta production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of JNK cascade / protein phosphatase inhibitor activity / negative regulation of phagocytosis / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / protein tyrosine kinase binding / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / cellular response to type II interferon / negative regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / cell migration / regulation of gene expression / protein phosphatase binding / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsGarcin, E.D. / Miller, T.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentMaryland Industrial Partnerships #5914
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA218259 United States
CitationJournal: Biorxiv / Year: 2025
Title: Engineering SIRP alpha conformational plasticity to reveal a cryptic pocket suitable for structure-based drug design.
Authors: Storder, M. / Barelier, S. / Cordier, F. / Yacoub, T. / Ilari, L. / Barral, K. / Mahmoodi, S. / Saez-Ayala, M. / Combes, S. / Betzi, S. / Derviaux, C. / Ulliana, A. / Torres, F. / Rubin, J. ...Authors: Storder, M. / Barelier, S. / Cordier, F. / Yacoub, T. / Ilari, L. / Barral, K. / Mahmoodi, S. / Saez-Ayala, M. / Combes, S. / Betzi, S. / Derviaux, C. / Ulliana, A. / Torres, F. / Rubin, J. / Roche, P. / Morelli, X. / Garcin, E.D. / Miller, T.W.
History
DepositionNov 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
B: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
C: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,40812
Polymers38,7583
Non-polymers6509
Water5,819323
1
A: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1815
Polymers12,9191
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1774
Polymers12,9191
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0503
Polymers12,9191
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.263, 57.263, 199.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-378-

HOH

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Components

#1: Protein Isoform 4 of Tyrosine-protein phosphatase non-receptor type substrate 1 / SHP substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / ...SHP substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like family member A / Inhibitory receptor SHPS-1 / Macrophage fusion receptor / MyD-1 antigen / Signal-regulatory protein alpha-1 / Sirp-alpha-1 / Signal-regulatory protein alpha-2 / Sirp-alpha-2 / Signal-regulatory protein alpha-3 / Sirp-alpha-3 / p84


Mass: 12919.462 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP / Variant: V2 / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B / References: UniProt: P78324
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01 M zinc sulfate heptahydrate, 0.1M MES monohydrate pH 6.5, and 25% (v/v) PEGMME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→43.36 Å / Num. obs: 76899 / % possible obs: 98.25 % / Redundancy: 8.9 % / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.032 / Χ2: 1.149 / Net I/σ(I): 8
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1613 / CC1/2: 0.554 / CC star: 0.844 / Rpim(I) all: 0.405 / Rrim(I) all: 0.841 / Χ2: 1.149 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→43.36 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.2303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 3700 4.81 %
Rwork0.1881 73199 -
obs0.1895 76899 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.6 Å2
Refinement stepCycle: LAST / Resolution: 1.63→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 17 323 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01072768
X-RAY DIFFRACTIONf_angle_d0.99743760
X-RAY DIFFRACTIONf_chiral_restr0.067422
X-RAY DIFFRACTIONf_plane_restr0.0094492
X-RAY DIFFRACTIONf_dihedral_angle_d16.01561023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.4406970.35292001X-RAY DIFFRACTION69.26
1.65-1.670.36471110.32132332X-RAY DIFFRACTION81.03
1.67-1.70.31361340.29772618X-RAY DIFFRACTION90.38
1.7-1.720.30161390.27762786X-RAY DIFFRACTION95.81
1.72-1.750.31091390.25242809X-RAY DIFFRACTION98.3
1.75-1.780.28791450.24262902X-RAY DIFFRACTION99.67
1.78-1.810.30461420.22452870X-RAY DIFFRACTION99.9
1.81-1.840.27331500.20922920X-RAY DIFFRACTION100
1.84-1.880.22951420.21152860X-RAY DIFFRACTION99.93
1.88-1.920.19961500.21362901X-RAY DIFFRACTION100
1.92-1.960.23611440.20742864X-RAY DIFFRACTION100
1.96-20.24821460.21232908X-RAY DIFFRACTION100
2-2.050.25631430.20812902X-RAY DIFFRACTION100
2.05-2.110.29511450.20012885X-RAY DIFFRACTION100
2.11-2.170.21711460.18922889X-RAY DIFFRACTION99.97
2.17-2.240.22811490.19122885X-RAY DIFFRACTION100
2.24-2.320.24881510.18662897X-RAY DIFFRACTION99.97
2.32-2.410.19991500.182880X-RAY DIFFRACTION100
2.41-2.520.21111500.18312885X-RAY DIFFRACTION100
2.52-2.660.18351440.18752887X-RAY DIFFRACTION100
2.66-2.820.21581440.19052879X-RAY DIFFRACTION100
2.82-3.040.22221430.18332888X-RAY DIFFRACTION99.97
3.04-3.350.20831500.17892905X-RAY DIFFRACTION99.9
3.35-3.830.20131440.16442906X-RAY DIFFRACTION99.9
3.83-4.830.18521510.15012860X-RAY DIFFRACTION99.8
4.83-43.360.17741510.18492880X-RAY DIFFRACTION99.77

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