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- PDB-9sid: Crystal structure of human Signal Regulatory Protein 2 (SIRP) alp... -

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Entry
Database: PDB / ID: 9sid
TitleCrystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 - Q52F mutant
Componentshuman SIRP alpha V2 - Q52F
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / SIRP / SIRPA / CD47 / DON'T EAT ME SIGNAL / IMMUNE CHECKPOINT
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsBarelier, S. / Betzi, S. / Garcin, E.D. / Miller, T.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) 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
DepositionAug 28, 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

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Assembly

Deposited unit
A: human SIRP alpha V2 - Q52F
B: human SIRP alpha V2 - Q52F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3347
Polymers25,8772
Non-polymers4575
Water1,62190
1
A: human SIRP alpha V2 - Q52F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1354
Polymers12,9391
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: human SIRP alpha V2 - Q52F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1993
Polymers12,9391
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.535, 58.049, 66.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein human SIRP alpha V2 - Q52F


Mass: 12938.507 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01M Zinc sulfate heptahydrate 0.1M MES monohydrate pH 6.5 25% v/v PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980103289881 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980103289881 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 25431 / % possible obs: 99.8 % / Redundancy: 12.3 % / CC1/2: 0.997 / Net I/σ(I): 9.95
Reflection shellResolution: 1.69→1.8 Å / Redundancy: 9.39 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4008 / CC1/2: 0.285 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→43.8 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1272 5 %
Rwork0.2392 --
obs0.2409 25416 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 16 90 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071783
X-RAY DIFFRACTIONf_angle_d0.9612416
X-RAY DIFFRACTIONf_dihedral_angle_d8.224249
X-RAY DIFFRACTIONf_chiral_restr0.064269
X-RAY DIFFRACTIONf_plane_restr0.009312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.760.45671380.41912603X-RAY DIFFRACTION98
1.76-1.840.31791380.32122634X-RAY DIFFRACTION100
1.84-1.940.32071400.28542647X-RAY DIFFRACTION100
1.94-2.060.3151390.27682653X-RAY DIFFRACTION100
2.06-2.220.29821400.27212662X-RAY DIFFRACTION100
2.22-2.440.29121410.23862675X-RAY DIFFRACTION100
2.44-2.80.27151420.23952696X-RAY DIFFRACTION100
2.8-3.520.24931440.22852730X-RAY DIFFRACTION100
3.52-43.80.24041500.19942844X-RAY DIFFRACTION100

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