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

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Basic information

Entry
Database: PDB / ID: 9sic
TitleCrystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 - Q52A mutant
Componentshuman SIRP alpha V2 - Q52A mutant
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: 1.5 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 - Q52A mutant
B: human SIRP alpha V2 - Q52A mutant
C: human SIRP alpha V2 - Q52A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9148
Polymers38,5873
Non-polymers3275
Water5,693316
1
A: human SIRP alpha V2 - Q52A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,8621
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: human SIRP alpha V2 - Q52A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,8621
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: human SIRP alpha V2 - Q52A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9282
Polymers12,8621
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.287, 57.287, 200.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-402-

HOH

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Components

#1: Protein human SIRP alpha V2 - Q52A mutant


Mass: 12862.410 Da / Num. of mol.: 3
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.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 42.31 %
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 1 / Wavelength: 0.978565037251 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565037251 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 54492 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 0.999 / Net I/σ(I): 32.64
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8625 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.29 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21625 2725 5 %RANDOM
Rwork0.17902 ---
obs0.18089 51767 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.597 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0 Å2-0 Å2
2---1.54 Å20 Å2
3---3.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 5 316 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162535
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.663664
X-RAY DIFFRACTIONr_angle_other_deg0.4381.575883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.635517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4210446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7581.9461384
X-RAY DIFFRACTIONr_mcbond_other4.7521.9451384
X-RAY DIFFRACTIONr_mcangle_it7.2723.4921725
X-RAY DIFFRACTIONr_mcangle_other7.2713.4931726
X-RAY DIFFRACTIONr_scbond_it5.4772.211313
X-RAY DIFFRACTIONr_scbond_other5.4752.2111314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1633.921936
X-RAY DIFFRACTIONr_long_range_B_refined14.84925.452881
X-RAY DIFFRACTIONr_long_range_B_other14.08624.232812
X-RAY DIFFRACTIONr_rigid_bond_restr3.14335232
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 196 -
Rwork0.174 3729 -
obs--99.72 %

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