PDB-4i2x: Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma)...

ID or keywords:

Entry

Database: PDB / ID: 4i2x

Title

Crystal structure of Signal Regulatory Protein gamma (SIRP-gamma) in complex with FabOX117

Components

FabOX117 heavy chain
FabOX117 light chain
Signal-regulatory protein gamma

Keywords

IMMUNE SYSTEM / Protein-Fab complex /

Structural Genomics /

Oxford Protein Production Facility / OPPF / Signal Regulatory Protein /

CD47 /

cell surface

Function / homology

Function and homology information

positive regulation of cell-cell adhesion / Signal regulatory protein family interactions / positive regulation of phagocytosis / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cell-cell signaling /

cell adhesion / intracellular signal transduction / negative regulation of cell population proliferation / positive regulation of cell population proliferation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Nettleship, J.E. / Ren, J. / Stuart, D.I. / Owens, R.J. / Oxford Protein Production Facility (OPPF)

Citation

Journal: Bmc Struct.Biol. / Year: 2013
Title: Crystal structure of signal regulatory protein gamma (SIRP gamma) in complex with an antibody Fab fragment.
Authors: Nettleship, J.E. / Ren, J. / Scott, D.J. / Rahman, N. / Hatherley, D. / Zhao, Y. / Stuart, D.I. / Barclay, A.N. / Owens, R.J.

History

Deposition	Nov 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2014	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4i2x.cif.gz	591.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i2/4i2x ftp://data.pdbj.org/pub/pdb/validation_reports/i2/4i2x	HTTPS FTP

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Related structure data

Related structure data	2wngS 3difS S: Starting model for refinement
Similar structure data	6sgy-d 1i8l-d 5w0k-2 5c0r-d 6oz4-d 6e3h-d 5oup-1 2jas-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: FabOX117 light chain

B: FabOX117 heavy chain

C: FabOX117 light chain

D: FabOX117 heavy chain

E: Signal-regulatory protein gamma

F: Signal-regulatory protein gamma

hetero molecules

171 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: FabOX117 light chain

B: FabOX117 heavy chain

E: Signal-regulatory protein gamma

hetero molecules

defined by author
85.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: FabOX117 light chain

D: FabOX117 heavy chain

F: Signal-regulatory protein gamma

hetero molecules

defined by author
85.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.361, 174.191, 81.734
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.171083, 0.98521, 0.009576), (0.979957, 0.171161, -0.10192), (-0.102052, -0.008053, -0.994746)	12.9437, -9.8963, 17.8422

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Antibody , 3 types, 6 molecules ACBDEF

#1: Antibody	FabOX117 light chain Mass: 23660.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody	FabOX117 heavy chain Mass: 24772.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody	Signal-regulatory protein gamma / SIRP-gamma / CD172 antigen-like family member B / Signal-regulatory protein beta-2 / SIRP-b2 / SIRP-beta-2 Mass: 36575.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P1W8

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Sugars , 1 types, 2 molecules

#6: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 3 types, 305 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.14 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate tetrahydrate, 20 % w/v polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 71197 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / R_merge(I) obs: 0.157 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 7000 / % possible all: 100

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3DIF, 2WNG

3dif

2wng

Resolution: 2.48→29.82 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.909 / SU B: 22.005 / SU ML: 0.231 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25996	3594	5.1 %	RANDOM
R_work	0.19571	-	-	-
obs	0.19891	67546	98.99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 61.151 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.89 Å²	-0 Å²	-0 Å²
2-	-	0.07 Å²	0 Å²
3-	-	-	-2.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.48→29.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11480	0	31	302	11813

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	11813
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.147	1.944	16112
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.053	5	1477
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.755	24.083	480
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.359	15	1879
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.617	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1824
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	8907
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.479→2.543 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.393	250	-
R_work	0.348	4336	-
obs	-	-	87.75 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.4524	0.4918	0.238	2.2918	0.9276	2.0167	-0.1183	0.0374	-0.0292	-0.0929	0.2958	-0.3167	-0.2236	0.3439	-0.1775	0.0521	-0.004	-0.0225	0.14	-0.0697	0.1998	29.72	42.515	18.057
2	0.7516	0.3333	-0.952	1.0238	0.6341	5.12	0.0423	-0.304	0.0399	0.4094	0.1371	-0.3903	-0.1637	0.2279	-0.1794	0.3195	0.1947	-0.2685	0.3146	-0.1914	0.3078	35.496	54.053	53.557
3	0.9446	-0.3348	-0.1627	2.3081	1.479	3.1245	0.0329	-0.0511	0.0277	0.155	-0.0513	0.1167	0.0682	-0.2423	0.0184	0.0616	0.0351	-0.0313	0.0815	0.0054	0.1449	9.029	40.169	25.198
4	0.9759	1.5349	0.7692	2.5172	1.2957	2.9849	0.1154	-0.0826	0.1151	0.2785	0.0637	0.0209	0.0758	0.1745	-0.1791	0.2713	0.1698	-0.2002	0.3699	-0.2243	0.4033	22.816	61.023	50.921
5	2.0435	1.3157	-1.6803	2.3648	-0.8117	2.4268	0.1108	-0.2234	0.2526	-0.0061	0.0719	0.1141	-0.1202	0.123	-0.1827	0.0111	-0.032	0.019	0.1888	-0.0769	0.1922	48.596	25.609	-5.449
6	1.9207	0.9969	0.6635	2.1767	0.165	3.3099	-0.3474	0.4168	0.5032	-0.781	0.2371	0.5064	-0.0032	-0.4978	0.1103	0.2976	-0.1294	-0.1514	0.3367	0.1001	0.2729	55.045	32.773	-41.832
7	1.5619	0.5169	-1.0681	1.2303	-0.3332	3.0514	-0.3087	-0.0761	-0.2586	-0.0684	0.2225	-0.1179	0.3445	0.218	0.0862	0.0797	0.0384	0.0107	0.1527	-0.0138	0.1643	48.747	4.728	-12.35
8	4.1684	3.2675	-0.6672	3.9309	-0.4958	1.4244	-0.3503	0.2548	-0.0218	-0.4425	0.2702	-0.1996	0.3772	-0.0257	0.0801	0.1803	-0.1281	0.0541	0.2333	-0.0585	0.1133	63.751	20.622	-37.568
9	1.5168	-0.673	-0.131	3.4754	-0.084	2.2638	0.0735	0.4835	-0.0614	-0.4189	-0.1479	0.3013	-0.255	-0.4113	0.0744	0.1118	0.0868	-0.0921	0.3044	-0.0447	0.1169	4.39	32.058	0.502
10	0.4206	-0.4273	0.4456	1.3015	-0.6516	2.7177	-0.0041	-0.0163	-0.0405	0.1862	-0.038	0.0065	-0.1533	0.082	0.0421	0.1745	0.0221	-0.03	0.1246	-0.015	0.0698	24.635	9.451	30.742
11	2.7979	-0.9559	0.8954	5.8129	-1.9977	1.66	-0.137	-0.6454	-0.3791	1.0408	0.2676	0.333	-0.0878	0.0141	-0.1305	0.6077	0.1115	0.0692	0.295	0.1016	0.2211	24.995	-13.498	62.496
12	2.5469	-0.6681	-0.0571	2.3798	-0.7723	2.5008	0.005	-0.4653	-0.2266	0.4736	-0.0519	-0.2348	0.2753	0.4303	0.0469	0.2608	0.0971	-0.0416	0.3366	0.1092	0.1279	43.16	-0.669	12.844
13	1.3829	-0.1994	0.5259	0.2223	-0.1585	5.8606	0.0215	0.1278	0.1235	-0.2366	-0.0416	0.0156	-0.2236	-0.4209	0.0201	0.3085	0.0643	-0.0023	0.1983	0.0236	0.1949	17.059	15.613	-16.753
14	8.18	0.0783	4.3686	3.6236	3.8091	7.5626	0.3158	0.8124	-0.5941	-0.8523	-0.8212	1.3779	-0.1884	-1.7822	0.5054	1.1835	0.0461	-0.4268	1.9998	0.145	1.1635	-6.362	11.777	-48.08

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 108
2	X-RAY DIFFRACTION	2	A	109 - 214
3	X-RAY DIFFRACTION	3	B	1 - 119
4	X-RAY DIFFRACTION	4	B	120 - 229
5	X-RAY DIFFRACTION	5	C	1 - 108
6	X-RAY DIFFRACTION	6	C	109 - 214
7	X-RAY DIFFRACTION	7	D	1 - 119
8	X-RAY DIFFRACTION	8	D	120 - 219
9	X-RAY DIFFRACTION	9	E	2 - 115
10	X-RAY DIFFRACTION	10	E	116 - 221
11	X-RAY DIFFRACTION	11	E	222 - 317
12	X-RAY DIFFRACTION	12	F	2 - 115
13	X-RAY DIFFRACTION	13	F	116 - 221
14	X-RAY DIFFRACTION	14	F	222 - 315

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