PDB-6vry: Structure of NCI09 fab in complex with SIV V2 peptide

ID or keywords:

Entry

Database: PDB / ID: 6vry

Title

Structure of NCI09 fab in complex with SIV V2 peptide

Components

NCI09 heavy chain
NCI09 light chain
SIV V2 peptide

Keywords

IMMUNE SYSTEM / SIV / V1V2 / V2 / Env /

gp120 /

antibody / NCI09

Function / homology

Function and homology information

membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell /

viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity /

membrane
Similarity search - Function

Biological species

Macaca mulatta (Rhesus monkey)

Simian immunodeficiency virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Gorman, J. / Ahmadi, M. / Kwong, P.D.

Citation

Journal: Iscience / Year: 2020
Title: HIV vaccine candidate with V1 deletion reveals virus vulnerability to V2 antibodies
Authors: Gorman, J. / Ahmadi, M. / Kwong, P.D.

History

Deposition	Feb 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vry.cif.gz	280.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vr/6vry ftp://data.pdbj.org/pub/pdb/validation_reports/vr/6vry	HTTPS FTP

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Related structure data

Related structure data	5wt9S S: Starting model for refinement
Similar structure data	6db7-2 2r2b-d 6vi2-1 3hzy-d 4m6o-d 6e8v-4 3okl-d 4xmk-2 3okk-d 2r1x-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) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5)

Deposited unit

L: NCI09 light chain

G: SIV V2 peptide

H: NCI09 heavy chain

hetero molecules

51.4 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)	65.760, 72.087, 100.833
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody

NCI09 light chain

Mass: 23439.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host:

Homo sapiens (human)

#2: Protein/peptide

SIV V2 peptide

Mass: 1965.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.)

Simian immunodeficiency virus / References: UniProt: P08810

#3: Antibody

NCI09 heavy chain

Mass: 25230.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host:

Homo sapiens (human)

#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-	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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.88 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 22% w/v PEG4000, 0.1 M sodium acetate, pH 4.6, cryoprotectant: 20% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 28, 2017

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.4→40 Å / Num. obs: 87297 / % possible obs: 92 % / Redundancy: 3.4 % / R_merge(I) obs: 0.044 / R_pim(I) all: 0.024 / R_rim(I) all: 0.05 / Χ²: 0.757 / Net I/σ(I): 17.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.4-1.42	1.6	0.414	3051	0.655	0.347	0.544	0.88	65.8
1.42-1.45	1.8	0.394	3480	0.724	0.317	0.509	0.885	74.2
1.45-1.48	2	0.343	3785	0.774	0.259	0.432	0.876	80.4
1.48-1.51	2.2	0.285	4053	0.838	0.204	0.352	0.913	86.2
1.51-1.54	2.5	0.229	4308	0.891	0.156	0.279	0.905	91.9
1.54-1.58	3	0.199	4453	0.939	0.124	0.236	0.889	95.1
1.58-1.62	3.7	0.167	4530	0.968	0.089	0.19	0.865	96.5
1.62-1.66	3.8	0.143	4570	0.974	0.075	0.162	0.831	97.2
1.66-1.71	3.8	0.11	4614	0.982	0.057	0.124	0.776	97.3
1.71-1.76	3.8	0.087	4562	0.986	0.045	0.098	0.746	97.4
1.76-1.83	3.8	0.067	4633	0.988	0.035	0.076	0.699	97.9
1.83-1.9	3.8	0.056	4619	0.99	0.029	0.064	0.704	97.8
1.9-1.99	3.8	0.048	4645	0.991	0.025	0.055	0.716	98.3
1.99-2.09	3.8	0.045	4640	0.991	0.023	0.05	0.772	97.9
2.09-2.22	3.8	0.041	4653	0.991	0.022	0.047	0.743	97.9
2.22-2.39	3.8	0.037	4640	0.992	0.019	0.041	0.658	97.6
2.39-2.63	3.8	0.033	4663	0.993	0.017	0.037	0.659	97.1
2.63-3.02	3.8	0.037	4615	0.992	0.019	0.042	0.828	96.2
3.02-3.8	3.8	0.032	4584	0.994	0.017	0.036	0.722	94.4
3.8-40	3.8	0.03	4199	0.994	0.016	0.035	0.568	82.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5WT9

5wt9

Resolution: 1.4→31.26 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.25

	R_factor	Num. reflection	% reflection
R_free	0.168	4175	5 %
R_work	0.1474	-	-
obs	0.1484	83495	88.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.4→31.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3433	0	49	634	4116

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3671
X-RAY DIFFRACTION	f_angle_d	1.127	5041
X-RAY DIFFRACTION	f_dihedral_angle_d	17.811	1378
X-RAY DIFFRACTION	f_chiral_restr	0.09	583
X-RAY DIFFRACTION	f_plane_restr	0.007	636

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 (%)
1.4001-1.416	0.1899	55	0.2102	1049	X-RAY DIFFRACTION	36
1.416-1.4326	0.2382	70	0.197	1330	X-RAY DIFFRACTION	45
1.4326-1.4501	0.2104	82	0.2084	1552	X-RAY DIFFRACTION	53
1.4501-1.4685	0.2424	97	0.1959	1843	X-RAY DIFFRACTION	62
1.4685-1.4878	0.1837	110	0.195	2078	X-RAY DIFFRACTION	70
1.4878-1.5082	0.227	121	0.1885	2319	X-RAY DIFFRACTION	77
1.5082-1.5297	0.2079	138	0.1825	2616	X-RAY DIFFRACTION	88
1.5297-1.5526	0.1957	144	0.1673	2743	X-RAY DIFFRACTION	93
1.5526-1.5768	0.2054	149	0.1663	2829	X-RAY DIFFRACTION	95
1.5768-1.6027	0.1731	153	0.1588	2902	X-RAY DIFFRACTION	96
1.6027-1.6303	0.1977	152	0.1529	2889	X-RAY DIFFRACTION	97
1.6303-1.6599	0.206	151	0.1544	2868	X-RAY DIFFRACTION	97
1.6599-1.6919	0.1712	154	0.1518	2911	X-RAY DIFFRACTION	97
1.6919-1.7264	0.1741	152	0.1528	2915	X-RAY DIFFRACTION	97
1.7264-1.7639	0.157	153	0.1517	2894	X-RAY DIFFRACTION	97
1.7639-1.805	0.1806	154	0.143	2936	X-RAY DIFFRACTION	98
1.805-1.8501	0.1765	155	0.1439	2930	X-RAY DIFFRACTION	98
1.8501-1.9001	0.1511	153	0.1377	2924	X-RAY DIFFRACTION	98
1.9001-1.956	0.1429	155	0.1441	2929	X-RAY DIFFRACTION	98
1.956-2.0191	0.1622	155	0.1374	2943	X-RAY DIFFRACTION	98
2.0191-2.0913	0.1616	155	0.1385	2938	X-RAY DIFFRACTION	98
2.0913-2.175	0.1434	155	0.1388	2958	X-RAY DIFFRACTION	98
2.175-2.274	0.1615	155	0.1336	2941	X-RAY DIFFRACTION	97
2.274-2.3938	0.1607	154	0.1349	2924	X-RAY DIFFRACTION	98
2.3938-2.5437	0.169	155	0.1418	2963	X-RAY DIFFRACTION	97
2.5437-2.74	0.1629	155	0.1463	2944	X-RAY DIFFRACTION	97
2.74-3.0156	0.1575	154	0.1461	2921	X-RAY DIFFRACTION	96
3.0156-3.4514	0.155	155	0.1422	2930	X-RAY DIFFRACTION	95
3.4514-4.3466	0.1532	148	0.1309	2816	X-RAY DIFFRACTION	91
4.3466-31.26	0.1953	136	0.171	2585	X-RAY DIFFRACTION	80

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	0.3193	-0.2455	-0.1764	0.5675	-0.4374	1.4575	0.0686	-0.0001	0.1003	0.0639	-0.0302	0.0534	-0.203	0.0275	-0.0016	0.1145	-0.0087	0.0058	0.0916	-0.0028	0.105	7.2313	-10.3714	-13.0497
2	1.1886	-0.0223	0.3421	1.5428	0.0813	1.0734	-0.0055	0.162	0.0108	-0.0947	0.0151	-0.0102	0.029	-0.0086	0.0001	0.1034	-0.0108	0.0065	0.1212	0.0102	0.1122	10.6849	-9.1716	-49.4856
3	0.1623	-0.0583	-0.0087	0.1991	0.0871	0.0605	-0.0155	-0.4821	-0.2293	0.3249	0.0277	-0.0559	0.0179	-0.1681	-0.0049	0.1571	-0.0111	-0.0391	0.2174	0.0478	0.1315	16.098	-27.0293	4.1564
4	0.5994	-0.095	0.0854	0.8413	0.2189	1.6398	0.004	-0.0244	-0.0477	-0.0013	0.0056	-0.069	0.0238	0.0606	0.0001	0.0803	-0.0068	-0.0089	0.0835	0.0074	0.0908	17.6407	-30.6282	-15.5345
5	1.2895	-0.004	0.1554	1.2604	-0.0729	0.7164	-0.0886	0.0705	0.0761	-0.092	0.0383	-0.0873	0.0296	0.082	-0	0.1163	0.0034	0.0101	0.1188	-0.0056	0.1089	23.4342	-15.415	-42.8262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 113 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 114 through 214 )
3	X-RAY DIFFRACTION	3	chain 'G' and (resid 163 through 173 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 1 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 214 )

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