PDB-8fbw: Crystal structure of SIV-1 V2 antibody NCI05 in complex with a V2...

ID or keywords:

Entry

Database: PDB / ID: 8fbw

Title

Crystal structure of SIV-1 V2 antibody NCI05 in complex with a V2 peptide

Components

Heavy chain of anti-SIV V2 antibody NCI05
Light chain of anti-SIV V2 antibody NCI05
SIV V2 peptide

Keywords

IMMUNE SYSTEM/VIRAL PROTEIN / SIV / antibody / NCI05 / V2 / variable loop 2 / SIVmac251 / IMMUNE SYSTEM-VIRAL PROTEIN complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION

Function and homology information

Biological species

Macaca mulatta (Rhesus monkey)

Simian immunodeficiency virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Zhou, T. / Kwong, P.D. / Van Wazer, D.J.

Funding support

United States, 1items

Citation

Journal: J.Virol. / Year: 2023
Title: Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or beta-Sheet Conformations on Time of SIV mac251 Acquisition.
Authors: Stamos, J.D. / Rahman, M.A. / Gorini, G. / Silva de Castro, I. / Becerra-Flores, M. / Van Wazer, D.J. / N'Guessan, K.F. / Clark, N.M. / Bissa, M. / Gutowska, A. / Mason, R.D. / Kim, J. / ...

History

Deposition	Nov 30, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 2, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 1, 2024	Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fbw.cif.gz	370 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8fbw_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8fbw_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8fbw_validation.xml.gz	36.5 KB	Display
Data in CIF	8fbw_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbw ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&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

C: Heavy chain of anti-SIV V2 antibody NCI05

D: Light chain of anti-SIV V2 antibody NCI05

E: SIV V2 peptide

A: Heavy chain of anti-SIV V2 antibody NCI05

B: Light chain of anti-SIV V2 antibody NCI05

F: SIV V2 peptide

hetero molecules

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

1

C: Heavy chain of anti-SIV V2 antibody NCI05

D: Light chain of anti-SIV V2 antibody NCI05

E: SIV V2 peptide

hetero molecules

defined by author&software
Evidence: gel filtration
50.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Heavy chain of anti-SIV V2 antibody NCI05

B: Light chain of anti-SIV V2 antibody NCI05

F: SIV V2 peptide

hetero molecules

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

Unit cell

Length a, b, c (Å)	130.650, 130.650, 216.948
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide	SIV V2 peptide Mass: 2179.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus

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Antibody , 2 types, 4 molecules CADB

#1: Antibody	Heavy chain of anti-SIV V2 antibody NCI05 Mass: 24758.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody	Light chain of anti-SIV V2 antibody NCI05 Mass: 22696.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...

Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#5: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 268 molecules

#6: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.2 M sodium chloride, 28.5% PEG8000, 0.1 M phosphate/citrate, pH 4.2

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: Liquid nitrogen stream / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.35→50 Å / Num. obs: 46240 / % possible obs: 100 % / Redundancy: 22 % / R_merge(I) obs: 0.119 / Χ²: 0.035 / Net I/σ(I): 24.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.35-2.39	22.9	1.06	2275	0.326	1	100
2.39-2.43	12	0.893	4329	0.332	1	100
2.43-2.48	11.9	0.758	4261	0.342	1	100
2.48-2.53	11.8	0.683	4340	0.338	1	100
2.53-2.59	11.7	0.615	4285	0.345	1	100
2.59-2.65	11.5	0.541	4318	0.356	1	100
2.65-2.71	11	0.445	4310	0.387	1	100
2.71-2.79	10.2	0.352	4328	0.409	1	100
2.79-2.87	12.1	0.309	4291	0.424	1	100
2.87-2.96	12.3	0.262	4323	0.462	1	100
2.96-3.07	12.3	0.214	4286	0.503	1	100
3.07-3.19	12.2	0.186	4346	0.546	1	100
3.19-3.33	12.1	0.147	4306	0.606	1	100
3.33-3.51	11.9	0.119	4305	0.704	1	100
3.51-3.73	11.6	0.102	4328	0.802	1	100
3.73-4.02	10.6	0.089	4300	0.889	1	100
4.02-4.42	12	0.071	4309	0.955	1	100
4.42-5.06	12.6	0.062	4317	0.943	1	100
5.06-6.37	12.2	0.057	4317	0.747	1	100
6.37-10	11.5	0.044	4344	0.756	1	100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487-000	refinement
SCALEPACK		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→48.91 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2462	2000	4.39 %
R_work	0.1941	-	-
obs	0.1963	45518	98.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.35→48.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6948	0	107	264	7319

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.554
X-RAY DIFFRACTION	f_dihedral_angle_d	7.439	1046
X-RAY DIFFRACTION	f_chiral_restr	0.043	1105
X-RAY DIFFRACTION	f_plane_restr	0.004	1246

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 (%)
2.35-2.41	0.3043	136	0.2342	2962	X-RAY DIFFRACTION	95
2.41-2.47	0.2707	136	0.2328	2976	X-RAY DIFFRACTION	97
2.47-2.55	0.3008	139	0.2307	2995	X-RAY DIFFRACTION	97
2.55-2.63	0.3863	139	0.2529	3033	X-RAY DIFFRACTION	98
2.63-2.72	0.2626	140	0.2265	3043	X-RAY DIFFRACTION	98
2.72-2.83	0.2887	140	0.2078	3058	X-RAY DIFFRACTION	99
2.83-2.96	0.287	141	0.213	3070	X-RAY DIFFRACTION	99
2.96-3.12	0.2499	143	0.2204	3100	X-RAY DIFFRACTION	99
3.12-3.31	0.3214	143	0.22	3114	X-RAY DIFFRACTION	100
3.31-3.57	0.2434	145	0.1945	3153	X-RAY DIFFRACTION	100
3.57-3.93	0.2408	145	0.1845	3160	X-RAY DIFFRACTION	100
3.93-4.5	0.1933	147	0.1589	3189	X-RAY DIFFRACTION	100
4.5-5.66	0.1811	149	0.1623	3249	X-RAY DIFFRACTION	100
5.66-48.91	0.2577	157	0.1951	3416	X-RAY DIFFRACTION	100

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	0.2068	-0.3129	-0.0487	0.4245	0.2313	0.4434	-0.0147	-0.0013	0.0414	-0.0053	-0.0259	0.0802	0.115	0.2017	-0	0.2261	0.0338	-0.024	0.3916	-0.0333	0.2643	49.8872	-64.1499	-15.5868
2	0.1027	0.0419	0.1563	0.1078	0.0678	0.3021	-0.0273	0.0675	0.1834	-0.0416	-0.0233	-0.0071	-0.0831	0.1147	0	0.2371	-0.0554	-0.0115	0.3212	-0.0311	0.3346	42.5295	-39.1985	9.6972
3	0.0179	-0.0289	0.0589	0.1103	-0.1633	0.2534	0.0577	-0.1768	-0.0389	-0.047	-0.1753	0.1774	0.0792	0.0231	-0.0494	0.205	-0.0694	-0.0164	0.3031	-0.0703	0.336	38.832	-43.6393	16.7057
4	0.0194	0.0186	0.0163	0.0208	0.0088	0.0028	-0.0645	0.1191	0.1381	-0.217	0.1083	-0.0202	-0.409	0.1496	-0	0.6372	-0.0023	0.0064	0.4491	0.071	0.5198	45.5144	-40.3986	-27.946
5	0.0524	0.0182	0.0118	0.3134	-0.1506	0.2443	0.0519	0.1402	0.073	-0.3888	-0.0101	0.1513	-0.2698	0.1197	0.0001	0.4133	0.0241	-0.0339	0.4116	0.07	0.3278	42.8772	-50.2406	-28.0582
6	0.0212	-0.0145	0.0269	-0.0003	-0.0022	0.0145	-0.1172	0.0169	-0.0358	-0.0003	0.2041	-0.0602	-0.1498	-0.0776	-0.0001	0.4856	0.0528	-0.0444	0.4316	0.0588	0.385	39.2315	-33.1472	-16.3055
7	0.267	-0.2259	-0.1555	0.2694	0.1366	0.1262	0.0439	0.0417	0.0281	-0.0085	-0.0079	0.0131	-0.3436	-0.0347	0	0.4006	-0.0703	0.0021	0.3216	0.003	0.2788	48.6697	-28.512	5.9585
8	0.0273	-0.0325	-0.0013	0.0377	0.0053	0.0039	-0.0081	-0.0084	0.1114	-0.1317	-0.0507	0.064	-0.0594	-0.0404	0	0.7584	0.0375	0.0043	0.3573	-0.0234	0.285	44.5535	-20.7965	10.6501
9	0.0045	-0.0001	0.0096	-0.0004	-0.0007	0.0002	0.1201	0.0724	0.0184	-0.2272	0.3536	0.032	-0.0855	0.199	-0.0001	0.4953	0.104	-0.0219	0.6426	-0.0444	0.3384	57.245	-70.8887	-27.6439
10	0.0045	-0.0003	-0.0043	0.0027	-0.003	0.0038	0.0477	0.0077	-0.0487	0.0505	-0.0065	0.0085	-0.0117	0.0311	0	0.732	0.1549	-0.2597	0.6183	-0.0779	0.5392	52.6974	-83.0468	-28.2697
11	0.0541	-0.0986	0.0146	0.2322	-0.3589	1.0991	-0.2028	-0.4459	0.7295	-0.0628	0.0787	-0.045	-0.2765	-0.5916	0.0271	0.378	0.09	-0.0083	0.6163	-0.198	0.9289	12.2682	-29.2385	10.2264
12	0.0938	0.0648	-0.1755	0.3016	0.1232	0.7501	-0.0076	-0.114	0.6999	-0.0643	-0.0455	-0.2348	0.0309	-0.5747	-0.075	0.1838	0.0364	-0.0244	0.5858	-0.0086	0.9043	14.1807	-31.1994	5.1427
13	0.3075	-0.1692	-0.2643	0.43	-0.1972	0.6666	0.0947	-0.2113	-0.2329	-0.2633	-0.1631	-0.0247	0.5612	-0.1719	0.0399	0.4218	-0.2024	0.0594	0.4601	0.0345	0.3547	28.4948	-69.823	1.2579
14	0.0535	-0.0526	0.0254	0.3239	-0.0536	0.4184	0.0557	-0.0706	0.1444	0.1445	-0.0824	-0.1269	0.2498	-0.2904	0.009	0.2639	-0.1149	0.0174	0.529	-0.0491	0.3399	27.6956	-60.0208	6.8684
15	0.0308	0.0243	0.0232	0.0115	0.0045	0.0133	-0.2322	0.0025	0.1648	-0.0658	-0.2533	-0.0196	-0.2046	-0.1234	-0	0.4912	0.0633	-0.0629	0.9959	-0.0147	0.8919	7.5156	-36.1766	-17.3805
16	0.0606	0.0253	-0.0371	0.0235	-0.0418	0.1537	-0.1622	0.1249	0.1818	-0.3155	-0.0278	0.2769	-0.422	0.0301	-0.0831	0.6061	0.2496	-0.1432	0.5946	0.1251	0.9297	13.8328	-26.6082	-11.4714
17	0.1016	-0.0405	-0.09	0.1553	-0.0836	0.1634	-0.112	0.0983	0.4902	-0.1643	-0.2002	0.4154	-0.1999	-0.2635	-0.0467	0.4989	0.2417	-0.1015	0.8726	0.0574	1.07	9.8396	-29.9589	-12.5457
18	0.0378	0.0107	-0.0513	0.1249	-0.0841	0.1298	-0.0498	-0.059	0.2078	-0.0434	-0.1516	0.0564	0.2252	-0.0778	0.0032	0.2592	-0.0111	0.0511	0.7682	0.097	0.5472	16.8268	-48.2211	-17.2075
19	0.379	-0.4892	0.0617	0.5829	-0.0988	-0.0063	0.1417	-0.0216	0.0951	-0.0803	-0.2289	-0.1827	0.3642	-0.2631	0.0339	0.3901	-0.2334	-0.0416	0.5927	0.0304	0.2867	18.2076	-67.8669	-1.4715
20	0.3216	-0.0064	0.1397	0.0143	0.0322	0.1759	0.2021	-0.4276	0.1409	0.1827	-0.0015	-0.1265	0.3101	-0.5511	0.4519	0.0109	-0.6781	-0.247	0.5968	-0.0326	0.2818	14.5076	-65.9868	-2.2209
21	0.3385	-0.1445	-0.1109	0.1784	-0.0632	0.1191	0.1884	0.0767	-0.0321	0.1908	-0.1453	0.0015	0.3871	-0.2585	0.111	0.635	-0.2423	-0.1433	0.444	-0.0177	0.4325	16.7612	-73.8599	-7.9979
22	0.0004	-0.0027	0.0035	0.0035	-0.0036	0.0011	0.0383	0.0091	-0.0272	0.1003	-0.1265	-0.0373	-0.0699	-0.0022	-0	1.0979	0.2147	0.0589	0.84	-0.2031	1.642	2.6957	-14.9752	7.2654
23	0.0014	-0.0011	-0.0002	0.0003	-0.0002	0.0006	0.0185	0.0094	0.0021	0.0001	0.0613	0.0016	0.0071	-0.0252	0	1.5771	0.1276	0.1174	1.653	0.0494	1.3011	8.3135	-5.7341	11.7806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 127 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 128 through 204 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 205 through 231 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 1 through 23 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 24 through 101 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 102 through 117 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 118 through 201 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 202 through 216 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 175 through 184 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 185 through 190 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 90 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 91 through 140 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 141 through 161 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 162 through 231 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1 through 23 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 24 through 62 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 63 through 101 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 102 through 117 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 118 through 154 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 155 through 191 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 192 through 214 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 175 through 184 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 185 through 189 )

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Protein/peptide , 1 types, 2 molecules EF

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Antibody , 2 types, 4 molecules CADB

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