PDB-4nzr: Crystal structure of the antibody-binding region of Protein M (Pr...

ID or keywords:

Entry

Database: PDB / ID: 4nzr

Title

Crystal structure of the antibody-binding region of Protein M (Protein M TD) in complex with anti-HIV antibody PGT135 Fab

Components

PGT135 heavy chain
PGT135 light chain
Protein M TD

Keywords

IMMUNE SYSTEM/PROTEIN BINDING / Leucine-rich repeat / broad antibody-binding / block antibody-antigen union / variable region / IMMUNE SYSTEM-PROTEIN BINDING complex

Function / homology

Function and homology information

membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Mycoplasma genitalium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Zhu, X. / Wilson, I.A.

Citation

Journal: Science / Year: 2014
Title: A structurally distinct human mycoplasma protein that generically blocks antigen-antibody union.
Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon ...
Abstract: We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known ...

History

Deposition	Dec 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nzr.cif.gz	493.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4nzr.ent.gz	411.7 KB	Display	PDB format
PDBx/mmJSON format	4nzr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nzr_validation.pdf.gz	453.1 KB	Display	wwPDB validaton report
Full document	4nzr_full_validation.pdf.gz	459.2 KB	Display
Data in XML	4nzr_validation.xml.gz	39.6 KB	Display
Data in CIF	4nzr_validation.cif.gz	60.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzr ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzr	HTTPS FTP

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Related structure data

Related structure data	5834C 5835C 5836C 4nztC 4nzuC 4jm4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5z68-2 4k8x-d 11995 6vc9-d 1lcy-2 4fm1-d 4v4e-7 4fm2-d 4nzt-d 6ayt-d 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)

Deposited unit

H: PGT135 heavy chain

L: PGT135 light chain

M: Protein M TD

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.599, 87.989, 130.184
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	PGT135 heavy chain Mass: 25385.594 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody	PGT135 light chain Mass: 23795.467 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein	Protein M TD / protein MG281 Mass: 46972.684 Da / Num. of mol.: 1 / Fragment: antibody-binding region (UNP residues 74-468) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG281 / Production host: Escherichia coli (E. coli) / References: UniProt: P47523
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.11 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.16 M sodium fluoride, 19% PEG3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013
Radiation	Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 95649 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / R_sym value: 0.08 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / R_sym value: 0.56 / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JM4

4jm4

Resolution: 1.65→34.966 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1862	4780	5 %	RANDOM
R_work	0.1542	-	-	-
obs	0.1558	95566	94.76 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.65→34.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6552	0	6	865	7423

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6743
X-RAY DIFFRACTION	f_angle_d	1.326	9157
X-RAY DIFFRACTION	f_dihedral_angle_d	13.088	2437
X-RAY DIFFRACTION	f_chiral_restr	0.079	1000
X-RAY DIFFRACTION	f_plane_restr	0.006	1186

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.6685	0.2833	141	0.2173	3109	X-RAY DIFFRACTION	98
1.6685-1.6881	0.2614	176	0.2117	3129	X-RAY DIFFRACTION	99
1.6881-1.7087	0.2577	166	0.2045	3117	X-RAY DIFFRACTION	99
1.7087-1.7303	0.2341	152	0.1999	3176	X-RAY DIFFRACTION	99
1.7303-1.7531	0.2368	172	0.1934	3122	X-RAY DIFFRACTION	99
1.7531-1.7771	0.2437	181	0.1961	3107	X-RAY DIFFRACTION	99
1.7771-1.8025	0.2099	127	0.1862	3157	X-RAY DIFFRACTION	99
1.8025-1.8294	0.2118	176	0.1739	3109	X-RAY DIFFRACTION	99
1.8294-1.858	0.1994	159	0.17	3138	X-RAY DIFFRACTION	99
1.858-1.8884	0.1992	158	0.164	3104	X-RAY DIFFRACTION	98
1.8884-1.921	0.186	176	0.166	3105	X-RAY DIFFRACTION	98
1.921-1.9559	0.2086	167	0.1572	3055	X-RAY DIFFRACTION	96
1.9559-1.9935	0.2123	163	0.1695	2939	X-RAY DIFFRACTION	94
1.9935-2.0342	0.1994	153	0.1662	2989	X-RAY DIFFRACTION	94
2.0342-2.0784	0.1861	176	0.15	3124	X-RAY DIFFRACTION	99
2.0784-2.1268	0.1815	172	0.1395	3108	X-RAY DIFFRACTION	99
2.1268-2.1799	0.1621	178	0.1347	3118	X-RAY DIFFRACTION	99
2.1799-2.2389	0.2044	161	0.1408	3151	X-RAY DIFFRACTION	98
2.2389-2.3047	0.1976	157	0.1383	3111	X-RAY DIFFRACTION	98
2.3047-2.3791	0.1944	165	0.145	3116	X-RAY DIFFRACTION	97
2.3791-2.4641	0.1702	168	0.146	3071	X-RAY DIFFRACTION	97
2.4641-2.5628	0.1735	133	0.1416	3151	X-RAY DIFFRACTION	98
2.5628-2.6794	0.1908	161	0.1478	3102	X-RAY DIFFRACTION	97
2.6794-2.8206	0.1803	156	0.1457	2890	X-RAY DIFFRACTION	90
2.8206-2.9972	0.1844	173	0.1477	2876	X-RAY DIFFRACTION	90
2.9972-3.2285	0.1849	181	0.1443	3072	X-RAY DIFFRACTION	96
3.2285-3.5531	0.1588	144	0.131	3085	X-RAY DIFFRACTION	94
3.5531-4.0665	0.1486	151	0.1374	2869	X-RAY DIFFRACTION	88
4.0665-5.1208	0.1442	129	0.1452	2419	X-RAY DIFFRACTION	74
5.1208-34.9735	0.2369	108	0.2165	2167	X-RAY DIFFRACTION	63

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	2.9569	0.8634	0.5547	3.1285	0.3397	2.7988	0.0329	0.0723	-0.0927	-0.1398	-0.059	0.1633	0.0211	-0.1526	0.0388	0.121	0.0358	-0.0017	0.104	-0.0055	0.1097	22.2277	61.6654	80.252
2	2.0788	-0.3056	0.1933	2.4482	-0.2004	3.1272	-0.0187	0.1121	-0.0843	-0.1577	-0.0136	0.2659	-0.0579	-0.2034	0.0584	0.0918	0.0232	0.0033	0.1128	0.0004	0.1117	22.4391	59.6076	79.8907
3	3.9689	-1.4094	-0.745	2.4718	0.8131	1.4806	0.1022	0.4274	0.3763	-0.4391	-0.1208	-0.2714	-0.2827	0.1074	0.0039	0.2628	-0.0125	-0.0018	0.225	0.0593	0.1891	55.9946	67.2561	87.6121
4	3.1809	-2.4983	-2.1048	1.9626	1.6416	1.4009	-0.176	-0.536	0.1729	0.3135	0.2881	-0.075	0.0088	0.1596	-0.0672	0.2232	0.0333	0.0005	0.1918	0.0087	0.1384	34.6815	40.7345	93.7746
5	5.0251	-0.5668	-1.2615	0.5699	-0.0484	1.6956	-0.0404	-0.1227	-0.1363	0.2551	0.0483	0.1333	0.028	-0.047	0.0015	0.1277	0.0091	0.0124	0.1081	-0.0039	0.1136	25.4337	41.6958	89.3918
6	1.9525	-1.6937	0.361	2.1683	1.0739	3.4888	-0.0841	0.025	-0.0373	-0.1242	-0.0114	-0.1265	-0.0652	0.0796	0.1233	0.0678	0.0095	0.0095	0.1034	0.026	0.0918	31.5167	42.7749	79.157
7	9.4143	-2.0249	-5.8464	3.0187	1.7236	5.5121	-0.1125	0.184	-0.1905	0.2622	0.021	0.0436	0.2213	-0.2039	0.0741	0.1263	0.0071	-0.0052	0.1351	0.0057	0.1294	27.597	35.4013	88.0104
8	3.6778	-1.8546	-0.1777	2.9342	0.442	0.9868	-0.0637	-0.1353	0.1083	0.0894	0.0706	-0.0094	0.0139	-0.0116	0.0061	0.131	-0.0108	0.0069	0.1056	0.0256	0.0705	29.6345	45.1106	87.1724
9	7.8615	0.6661	1.1318	0.2371	0.0729	0.2108	-0.1017	-0.1343	0.4076	0.1289	0.0081	-0.0328	-0.1293	-0.003	0.1371	0.1379	0.0089	-0.0229	0.1437	-0.0168	0.1429	50.6333	41.9668	92.5661
10	2.0716	-1.2501	-0.4977	1.5055	1.519	2.1029	0.2638	0.0703	0.4168	-0.5682	-0.1366	-0.7938	-0.3262	0.0644	-0.0861	0.1512	-0.0024	0.0393	0.1867	-0.0042	0.2651	64.0026	68.7397	97.5452
11	0.9551	1.8983	0.7373	7.7661	4.1782	2.4609	0.0745	-0.0354	0.0754	0.2998	-0.0899	0.0348	0.1843	-0.0665	0.0007	0.1315	0.0078	-0.0185	0.1501	-0.0085	0.1659	57.5177	55.2869	100.8246
12	1.5799	0.3301	1.1079	4.7929	3.0238	4.1667	-0.0098	-0.0819	-0.0171	-0.0046	-0.056	0.0346	-0.0309	-0.059	0.0517	0.0828	-0.0184	0.0109	0.1236	0.0151	0.097	54.2955	55.2008	98.4427
13	3.9422	1.3794	0.6366	8.1888	2.9643	4.0886	-0.0529	-0.2456	0.4893	0.335	-0.0865	-0.1154	-0.2649	0.1037	0.1088	0.1353	0.0087	-0.043	0.1299	-0.0162	0.1688	60.2821	69.631	105.3895
14	2.622	2.8369	1.4532	6.2857	2.8252	2.8624	0.1603	-0.0379	-0.1069	0.5053	0.0363	-0.7577	0.143	0.2249	-0.1347	0.157	0.0323	-0.0769	0.1795	-0.0246	0.2523	66.1774	57.0982	105.3534
15	1.51	0.4171	-0.1316	1.0429	0.0547	1.9854	0.0031	-0.0864	-0.0815	0.0596	-0.0039	0.0055	0.1599	-0.0191	-0.0082	0.1066	0.0207	0.0032	0.0771	0.0094	0.0919	50.2066	26.4715	78.9875
16	0.6419	-0.0937	-0.1002	1.9148	-0.8405	1.2408	-0.0048	0.0253	0.1027	-0.123	-0.0546	-0.2472	-0.0365	0.1804	0.0672	0.0937	-0.0221	0.0076	0.1481	-0.0004	0.14	68.1318	42.684	65.2903
17	2.4045	0.1483	0.0249	1.5615	-0.1658	0.9961	-0.0165	0.1754	0.194	-0.1691	0.0046	0.0532	-0.0722	-0.0479	0.0103	0.1349	-0.0128	0.011	0.1182	0.0275	0.1188	55.0893	46.6313	59.1642
18	2.0962	-0.0181	0.2653	0.9079	-0.0241	0.9973	0.0227	0.1583	0.0844	-0.1008	-0.0213	0.1412	-0.0389	-0.1752	-0.0019	0.1223	0.0111	0.0035	0.1474	0.0096	0.095	31.7052	40.1984	60.0135

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 66 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 67 through 109 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 110 through 228 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 18 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 19 through 38 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 39 through 61 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 62 through 75 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 76 through 101 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 102 through 113 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 114 through 128 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 129 through 150 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 151 through 174 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 175 through 188 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 189 through 214 )
15	X-RAY DIFFRACTION	15	chain 'M' and (resid 78 through 179 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 180 through 261 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 262 through 326 )
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 327 through 468 )

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