PDB-7l77: Crystal structure of broadly HIV-1-neutralizing antibody VRC33.01

ID or keywords:

Entry

Database: PDB / ID: 7l77

Title

Crystal structure of broadly HIV-1-neutralizing antibody VRC33.01

Components

Heavy chain of VRC 33.01
Light chain of VRC33.01

Keywords

IMMUNE SYSTEM / broadly neutralizing antibody / vaccine-elicited / HIV-1

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.543 Å

Authors

Zhou, T. / Kwong, P.D.

Citation

Journal: Cell Rep / Year: 2021
Title: Crystal structure of broadly HIV-1-neutralizing antibody
Authors: Zhou, T.

History

Deposition	Dec 27, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7l77.cif.gz	265.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7l77.ent.gz	216.5 KB	Display	PDB format
PDBx/mmJSON format	7l77.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l7/7l77 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/7l77	HTTPS FTP

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Related structure data

Related structure data	7l79C 3se8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1rz8-2 5ijk-1 4r96-4 5mv3-8 5mu0-1 3g6j-3 6azm-2 5mv3-3 6tcp-1 6dwa-1 5mp5-4 5k9j-d 1mrc-d 1aj7-d 5vh4-1 7o30-2 6wrp-d 5mvj-4 6wj0-d 5ggq-d Search similar-shape structures by Omokage search (details) 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	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: Heavy chain of VRC 33.01

L: Light chain of VRC33.01

48 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.155, 70.839, 65.380
Angle α, β, γ (deg.)	90.000, 99.800, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Heavy chain of VRC 33.01 Mass: 24030.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody	Light chain of VRC33.01 Mass: 23977.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H₂O
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: 2.34 Å³/Da / Density % sol: 47.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 13% PEG3350, 10% Iso-propanol, Ammonium Citrate, pH 4.5

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Data collection

Diffraction

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

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 19, 2017

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.54→50 Å / Num. obs: 62505 / % possible obs: 96.4 % / Redundancy: 3.5 % / R_merge(I) obs: 0.079 / R_pim(I) all: 0.05 / R_rim(I) all: 0.093 / Χ²: 2.431 / Net I/σ(I): 9.9 / Num. measured all: 219175

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
1.54-1.57	2.8	0.52	2642	0.674	0.36	0.636	1.153	81.9
1.57-1.6	3.2	0.481	3064	0.709	0.309	0.574	1.161	95.2
1.6-1.63	3.5	0.442	3110	0.788	0.272	0.52	1.195	96.6
1.63-1.66	3.6	0.412	3120	0.815	0.252	0.484	1.341	96.5
1.66-1.69	3.6	0.342	3135	0.873	0.209	0.401	1.423	96.9
1.69-1.73	3.6	0.313	3116	0.885	0.192	0.368	1.705	97.1
1.73-1.78	3.6	0.267	3154	0.911	0.164	0.314	1.803	97.2
1.78-1.83	3.6	0.226	3131	0.938	0.139	0.265	1.993	96.9
1.83-1.88	3.6	0.2	3124	0.943	0.123	0.235	2.201	97.1
1.88-1.94	3.6	0.173	3125	0.961	0.108	0.204	2.507	97
1.94-2.01	3.6	0.146	3127	0.968	0.092	0.173	2.694	96.4
2.01-2.09	3.5	0.131	3158	0.973	0.082	0.155	2.837	97.2
2.09-2.19	3.5	0.116	3139	0.98	0.073	0.137	3.109	97.2
2.19-2.3	3.5	0.107	3140	0.981	0.067	0.126	3.259	97.3
2.3-2.44	3.5	0.096	3184	0.985	0.06	0.114	3.306	97.6
2.44-2.63	3.5	0.086	3192	0.987	0.054	0.102	3.354	98.2
2.63-2.9	3.5	0.075	3177	0.989	0.047	0.089	3.496	98.1
2.9-3.32	3.5	0.062	3204	0.992	0.039	0.073	3.402	98.1
3.32-4.18	3.5	0.051	3239	0.994	0.032	0.061	3.353	98.8
4.18-50	3.5	0.044	3224	0.996	0.028	0.052	2.668	96.8

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX	1.1	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SE8

3se8

Resolution: 1.543→29.214 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1865	2000	3.2 %
R_work	0.1517	60490	-
obs	0.1528	62490	96.1 %

Solvent computation

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

Displacement parameters

B_iso max: 233.52 Å² / B_iso mean: 27.9737 Å² / B_iso min: 9.71 Å²

Refinement step

Cycle: final / Resolution: 1.543→29.214 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3364	0	0	516	3880
B_iso mean	-	-	-	37.61	-
Num. residues	-	-	-	-	440

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.543-1.5812	0.2541	120	0.2321	3622	81
1.5812-1.6239	0.2135	142	0.2111	4300	96
1.6239-1.6717	0.2283	143	0.2018	4322	97
1.6717-1.7257	0.2363	143	0.1919	4349	97
1.7257-1.7874	0.2562	144	0.179	4331	97
1.7874-1.8589	0.2076	144	0.1756	4347	97
1.8589-1.9435	0.2335	143	0.1672	4348	97
1.9435-2.0459	0.177	145	0.1547	4389	97
2.0459-2.1741	0.1962	144	0.1507	4329	97
2.1741-2.3419	0.186	145	0.1489	4404	97
2.3419-2.5774	0.1746	146	0.1494	4392	98
2.5774-2.9501	0.1848	146	0.1489	4414	98
2.9501-3.7156	0.1543	147	0.1344	4470	98
3.7156-29.214	0.1745	148	0.1325	4473	98

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	4.0043	2.9502	0.3555	5.989	-0.3585	1.093	0.2274	-0.1953	0.1698	0.3068	-0.36	0.3321	0.0304	-0.2352	0.232	0.1095	0.0225	-0.0045	0.12	0.0272	0.1087	-40.1789	-1.7044	-2.9489
2	3.4269	-0.2519	0.0418	4.2777	-0.4793	1.3428	-0.0319	0.0973	0.0351	-0.0114	-0.0204	-0.1287	-0.0092	0.0336	0.0523	0.0831	-0.0006	-0.0069	0.0969	0.003	0.0633	-30.7047	4.2286	-6.3923
3	2.6213	-1.5456	1.1606	8.2924	-1.1194	1.6571	-0.0072	0.2542	-0.1214	-0.2682	-0.0666	-0.07	0.1372	0.1206	0.0621	0.1473	-0.0012	0.0114	0.1661	0.0263	0.0805	-31.6244	1.2305	-13.9444
4	0.7895	-0.5137	0.0963	6.4263	1.71	1.6608	0.051	0.0443	0.0658	-0.5202	-0.0178	0.0853	0.0104	-0.0493	-0.0023	0.1103	-0.0046	0.0111	0.1123	0.0152	0.1169	-36.0599	-4.78	-9.0819
5	4.4582	3.6607	-2.5804	3.3817	-1.6535	2.6999	0.1467	0.1218	0.2876	-0.0062	-0.014	0.0946	-0.2635	0.163	-0.2342	0.1399	0.0078	-0.0043	0.145	0.0325	0.1785	-24.3153	7.69	-5.1451
6	2.8665	1.8651	-0.961	1.6504	-0.9877	0.5298	-0.0158	0.0117	-0.0982	0.001	0.0007	-0.041	0.0538	0.0093	0.0188	0.1208	0.0046	-0.0099	0.1217	0.0014	0.1169	-36.9752	-5.4599	1.5457
7	2.7707	0.695	-0.8448	4.3519	-0.5653	0.7898	0.1841	-0.6209	-0.2757	0.7257	0.1214	-0.2727	0.1729	0.1302	-0.3682	0.2238	0.0312	-0.0214	0.2467	0.0113	0.1401	-46.093	-14.1187	30.9245
8	1.5141	-0.153	0.0699	1.8461	1.2118	3.6364	-0.0508	-0.0985	0.0941	0.1178	0.0404	-0.0891	-0.185	0.0357	0.0046	0.1012	-0.0018	-0.0057	0.1085	0.0048	0.1063	-42.7454	-10.0817	19.6877
9	2.284	-0.889	0.1069	3.4295	2.8444	2.3481	-0.0849	-0.2357	0.112	0.2008	0.0031	-0.0436	-0.1493	-0.3523	0.0808	0.1242	0.0215	-0.0033	0.1216	-0.0001	0.1324	-49.6936	-4.6403	21.0037
10	4.2749	-1.2359	0.8001	3.0065	2.0934	5.207	-0.1068	-0.3148	-0.0427	0.1855	0.0357	0.1756	0.1031	-0.6128	-0.1533	0.1041	-0.0001	0.0228	0.1857	0.0144	0.1473	-53.6867	-8.4008	21.4531
11	1.24	0.152	-1.4598	1.0451	-1.8013	5.9186	-0.0075	-0.0076	-0.0453	-0.0323	-0.0793	0.001	0.1618	0.2527	0.1153	0.0955	-0.004	-0.0042	0.1073	-0.0137	0.1129	-12.1544	-1.867	5.9335
12	2.8343	1.6187	2.1887	3.6536	0.8513	2.67	0.1067	-0.2248	0.2191	0.0808	-0.0546	0.2769	-0.1783	-0.2246	-0.1059	0.112	0.0246	0.0162	0.1068	0.0103	0.1362	-19.8073	7.3941	9.3479
13	2.2753	0.8092	-0.8822	1.3135	-0.4039	3.9427	0.0065	0.0619	-0.01	-0.0593	0.0043	-0.0795	-0.035	0.1397	-0.0153	0.0933	0.0319	0.0051	0.0533	0.0064	0.1174	-12.6471	1.6502	5.5756
14	3.7117	4.3465	-4.4658	5.0744	-5.2997	5.495	0.1757	-0.1888	-0.0334	0.1422	-0.1913	-0.0324	-0.0174	-0.032	0.1437	0.1153	0.0202	-0.014	0.1524	0.0062	0.1339	-20.4288	-9.1417	24.7064
15	8.0812	4.578	2.5562	5.7757	2.3809	4.1962	0.0777	-0.388	0.0762	-0.0527	-0.0665	0.3908	-0.0787	-0.431	0.1036	0.1083	0.0133	0.0258	0.1347	0.0288	0.118	-49.0554	-19.9505	26.1456
16	7.4483	5.4845	1.7581	5.3635	1.846	0.6134	-0.056	-0.0907	-0.2878	0.1349	0.0144	-0.2604	-0.0409	-0.0184	0.0773	0.108	-0.01	-0.0027	0.1506	0.0278	0.0575	-33.8013	-20.4705	26.7885
17	4.4334	4.1837	0.0861	5.7531	-0.4015	1.1466	-0.153	0.122	0.2251	-0.2088	0.1315	0.2311	-0.0279	0.1139	0.0139	0.0687	0.0318	0.0169	0.1303	0.0014	0.0779	-32.6191	-17.7676	23.7481
18	3.1065	3.9927	-0.5573	5.9776	-0.2282	4.8578	-0.1196	0.0145	-0.2823	-0.1843	0.1944	0.0988	0.3529	-0.2751	-0.0607	0.099	0.0077	-0.0244	0.1119	0.0555	0.1719	-46.4754	-27.7428	23.7612
19	4.4696	4.7037	0.9644	5.65	-0.0701	1.1264	0.3182	-0.6464	-0.5413	0.4147	-0.3632	-0.2137	-0.1111	0.0299	-0.0598	0.1772	-0.0134	-0.021	0.1976	0.0429	0.1102	-38.5641	-24.9585	34.454

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )	H	1 - 17
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 56 )	H	18 - 56
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 57 through 75 )	H	57 - 75
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 76 through 87 )	H	76 - 87
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 88 through 104 )	H	88 - 104
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 105 through 125 )	H	105 - 125
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 126 through 140 )	H	126 - 140
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 141 through 194 )	H	141 - 194
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 195 through 209 )	H	195 - 209
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 210 through 220 )	H	210 - 220
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 1 through 38 )	L	1 - 38
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 39 through 61 )	L	39 - 61
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 62 through 105 )	L	62 - 105
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 106 through 117 )	L	106 - 117
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 118 through 132 )	L	118 - 132
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 133 through 154 )	L	133 - 154
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 155 through 178 )	L	155 - 178
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 179 through 192 )	L	179 - 192
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 193 through 218 )	L	193 - 218

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