PDB-7l79: Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01

ID or keywords:

Entry

Database: PDB / ID: 7l79

Title

Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01

Components

Heavy chain of VRC40.01
Light chain of VRC40.01

Keywords

IMMUNE SYSTEM / Broadly neutralizing antibody / 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: 2.826 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 / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7l79.cif.gz	419.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7l79.ent.gz	348.8 KB	Display	PDB format
PDBx/mmJSON format	7l79.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l7/7l79 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/7l79	HTTPS FTP

-
Related structure data

Related structure data	7l77C 3se8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2o5z-d 6d11-1 1rzi-6 5bk3-3 6ubi-2 4uin-d 1y0l-1 4r7n-7 5chn-1 3w9d-1 4odu-2 3o2w-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 - HomologyF&H Search

-
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 VRC40.01

L: Light chain of VRC40.01

A: Heavy chain of VRC40.01

B: Light chain of VRC40.01

hetero molecules

97.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: Heavy chain of VRC40.01

L: Light chain of VRC40.01

hetero molecules

defined by author&software
Evidence: gel filtration
48.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Heavy chain of VRC40.01

B: Light chain of VRC40.01

hetero molecules

defined by author&software
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.792, 135.950, 136.908
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Heavy chain of VRC40.01 Mass: 24657.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody	Light chain of VRC40.01 Mass: 23616.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell (production host): HEK 293F / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10.6 % PEG 8000, 200 mM Zinc Acetate, Sodium Cacodylate, pH 6.5

-
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 225 mm CCD / Detector: CCD / Date: Feb 26, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 28072 / % possible obs: 98.5 % / Redundancy: 3.7 % / R_merge(I) obs: 0.206 / R_pim(I) all: 0.124 / R_rim(I) all: 0.241 / Χ²: 1.817 / Net I/σ(I): 4.2 / Num. measured all: 104728

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
2.8-2.85	3.3	0.796	1338	0.668	0.508	0.948	0.812	98
2.85-2.9	3.4	0.743	1384	0.714	0.466	0.88	0.825	98.1
2.9-2.96	3.5	0.721	1370	0.707	0.447	0.851	0.88	97.9
2.96-3.02	3.6	0.63	1360	0.77	0.382	0.739	0.945	98.5
3.02-3.08	3.7	0.591	1428	0.796	0.354	0.691	1.028	98.2
3.08-3.15	3.8	0.521	1348	0.866	0.307	0.607	1.13	98.5
3.15-3.23	3.9	0.485	1388	0.851	0.283	0.563	1.247	98.6
3.23-3.32	3.9	0.392	1376	0.918	0.226	0.453	1.388	98.6
3.32-3.42	4	0.359	1391	0.93	0.208	0.415	1.474	98.4
3.42-3.53	3.9	0.308	1383	0.944	0.179	0.357	1.65	98.8
3.53-3.65	3.9	0.288	1420	0.949	0.168	0.334	1.798	98.4
3.65-3.8	3.9	0.253	1387	0.957	0.148	0.293	1.983	99
3.8-3.97	3.9	0.229	1394	0.966	0.134	0.266	2.03	98.3
3.97-4.18	3.9	0.191	1405	0.971	0.114	0.223	2.362	99
4.18-4.44	3.8	0.158	1416	0.977	0.095	0.185	2.672	98.9
4.44-4.79	3.7	0.136	1429	0.981	0.083	0.16	2.74	98.6
4.79-5.27	3.7	0.131	1403	0.985	0.08	0.155	2.579	98.5
5.27-6.03	3.8	0.143	1443	0.977	0.088	0.169	2.527	99
6.03-7.59	3.7	0.135	1482	0.981	0.081	0.158	2.543	99
7.59-50	3.3	0.087	1527	0.991	0.055	0.103	3.256	97.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX	V1.1	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SE8

3se8

Resolution: 2.826→36.916 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2795	1394	4.99 %
R_work	0.2201	26566	-
obs	0.223	27960	96.99 %

Solvent computation

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

Displacement parameters

B_iso max: 165.48 Å² / B_iso mean: 54.4625 Å² / B_iso min: 23.33 Å²

Refinement step

Cycle: final / Resolution: 2.826→36.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6776	0	9	100	6885
B_iso mean	-	-	62.19	41.67	-
Num. residues	-	-	-	-	886

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 (%)
2.826-2.9267	0.378	126	0.3268	2258	84
2.9267-3.0438	0.4362	127	0.2931	2651	98
3.0438-3.1823	0.3051	151	0.2725	2635	98
3.1823-3.35	0.2981	134	0.2598	2666	99
3.35-3.5597	0.346	146	0.2331	2679	98
3.5597-3.8343	0.283	144	0.2177	2664	99
3.8343-4.2197	0.274	127	0.1993	2727	99
4.2197-4.8291	0.2131	148	0.1657	2712	99
4.8291-6.0798	0.2388	146	0.1866	2708	98
6.0798-36.916	0.2687	145	0.2269	2866	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	1.6809	-0.1126	0.3508	2.8845	-0.7085	1.6866	0.1363	0.0215	-0.1616	-0.0074	-0.0484	0.0457	-0.0019	-0.2537	-0.0001	0.3295	0.0225	-0.0087	0.3458	0.0359	0.3225	-3.048	2.1536	26.4641
2	1.6106	-0.9731	0.7748	2.8543	0.4742	1.4079	0.325	0.8181	0.0505	0.1947	0.0399	0.0006	-0.4291	-0.2255	0.0017	0.3764	-0.0071	-0.0213	0.4607	0.1669	0.4512	10.9313	30.0985	7.1615
3	2.0672	-0.7013	-0.0688	0.6874	-0.7379	1.1396	0.2295	0.9869	-0.084	-0.2793	-0.3274	-0.0509	-0.214	0.0044	-0.0023	0.486	0.0506	-0.0871	0.6536	0.1171	0.4442	11.9151	28.7102	3.2281
4	3.3072	-0.8876	-1.7523	2.6671	0.2931	1.444	-0.0654	0.1264	-0.054	0.2324	0.0753	-0.2443	0.0224	0.3523	0	0.2859	0.0077	-0.0654	0.2935	0.0045	0.3111	19.2776	-4.117	24.5999
5	1.5786	-0.2503	-0.6964	1.0869	-0.2065	0.4234	-0.0755	0.0933	-0.1101	0.1642	0.1815	-0.0167	0.5365	-0.344	-0.0001	0.3197	-0.0595	-0.0456	0.4183	-0.0677	0.3141	16.2677	-0.8625	24.8879
6	0.1924	-0.2667	-0.0277	0.3758	0.0762	1.0683	-0.2094	-0.1836	0.8127	-0.4454	0.3078	-0.3276	0.8551	0.0407	0.0319	0.4461	0.015	0.01	0.2737	0.0841	0.4619	29.3292	11.215	12.0145
7	1.5498	2.9262	0.5695	7.5135	2.7477	1.5944	-0.5469	0.8416	0.8589	-0.2765	-0.3571	1.2186	-0.507	-0.0352	-1.1209	0.6105	0.0276	-0.1844	0.5311	0.1668	0.3701	15.9368	38.1047	10.1237
8	1.0428	0.8168	0.2077	0.8446	-0.0252	1.0047	0.0153	-0.4674	0.0861	0.3074	0.0652	0.0992	-0.0933	0.0883	-0.0001	0.4374	-0.0411	-0.0159	0.3744	0.0351	0.3472	23.7516	26.2152	16.1117
9	0.213	-0.1997	0.0843	0.1759	-0.0938	0.1904	-0.3363	-0.0023	0.4803	-0.3425	0.2663	0.112	-0.5163	0.0876	-0.0022	0.2722	-0.1572	-0.1001	0.5379	0.0563	0.46	20.2365	31.5276	23.1491
10	1.1579	-1.8082	0.7568	3.2947	-0.8508	0.7416	0.2773	0.5969	-0.6173	-0.4081	-0.2322	-0.0306	0.2613	0.1026	1.118	-0.028	0.4738	-0.0163	0.8633	-0.3341	0.4733	22.9303	13.4686	7.3171
11	2.542	1.2756	2.5378	0.778	1.187	2.6008	-0.1419	-0.7004	0.8635	0.3322	-0.387	1.0152	-0.6137	-1.156	-0.0833	0.6845	0.0527	0.1245	0.468	-0.0157	0.5909	15.5477	38.6219	19.283
12	1.0284	0.2256	-1.0326	0.5887	0.2313	1.3953	0.4289	0.1105	0.3634	-0.3628	-0.1294	-0.3108	-0.3666	0.2403	0.0004	0.5317	-0.0584	0.0487	0.5345	0.0944	0.5838	28.6782	35.3701	16.317
13	1.6948	-1.6228	-0.0995	1.9844	-0.0398	1.9619	0.118	0.3278	0.045	0.0655	0.0483	0.2817	-0.1842	-0.299	-0.0025	0.3343	-0.0266	0.0311	0.3859	-0.0013	0.4032	-4.0122	34.6177	94.863
14	0.2459	0.2241	0.0383	0.2083	0.1759	0.8506	0.0815	0.0893	-0.08	-0.092	0.1262	0.6223	-0.0224	-0.0103	0.0001	0.3117	0.0244	0.0217	0.3583	0.0534	0.5222	2.7831	41.985	87.3346
15	0.8504	-0.0864	-0.6395	0.7799	-0.252	0.6639	0.2672	0.5172	0.7032	0.1718	0.0373	-0.3596	-0.2781	-0.0291	-0.0014	0.3979	-0.0812	0.0525	0.5202	0.1977	0.4307	18.9912	65.1879	71.9604
16	2.458	-0.2439	-1.3377	0.8456	0.2492	0.9113	-0.1376	0.6002	0.0057	-0.1469	0.1022	0.2882	-0.3557	0.0152	0.0002	0.6443	-0.1711	-0.0817	0.554	0.0729	0.3695	10.8344	59.5877	71.0722
17	2.8672	0.0727	-1.3612	3.7529	-0.6628	2.8548	-0.1155	0.0164	0.041	-0.0603	0.0817	-0.0641	-0.0619	0.2531	0.0035	0.2861	0.0016	0.0239	0.2765	-0.0155	0.376	18.6485	28.8508	92.83
18	0.8768	0.9649	-0.5857	1.1217	-0.3028	1.484	-0.1345	0.1701	0.1007	-0.3685	0.1384	-0.0173	-0.2851	-0.1301	0.0001	0.44	-0.0566	0.0165	0.4037	0.0004	0.3939	21.6895	58.4575	78.9552
19	0.0831	0.0454	-0.0658	0.7828	-0.0607	1.0547	-0.3155	-0.1795	-0.2043	-0.1329	-0.1409	0.179	0.1616	-0.3327	-0.0354	0.6185	-0.1262	0.0273	0.348	0.0166	0.3383	23.7302	58.0904	84.0298
20	0.525	-0.4175	0.3904	0.3003	-0.2713	0.2518	-0.4479	0.0806	-0.1109	0.2427	0.1436	-0.4719	-0.2321	0.1415	-0.0009	0.3827	-0.0889	-0.0299	0.6067	0.1455	0.307	20.1851	63.3729	91.0974
21	2.648	0.0929	1.4769	0.8786	-0.8965	1.8164	-0.3897	-0.1995	-0.11	-0.9975	0.5856	0.7793	-0.5905	0.1016	0.0065	0.4629	-0.1018	0.0474	0.3018	0.0932	0.3001	18.9514	59.2811	81.8951
22	1.6826	1.0654	-0.5836	0.7554	-0.1214	1.009	0.3585	-0.0634	-0.0129	-1.1752	0.2143	0.0201	-0.6214	0.3817	0.0154	0.612	-0.0432	0.0678	0.4291	0.0584	0.3409	28.6127	67.2053	84.1744

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 125 )	H	1 - 125
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 126 through 171 )	H	126 - 171
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 172 through 229 )	H	172 - 229
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 75 )	L	1 - 75
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 76 through 102 )	L	76 - 102
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 103 through 113 )	L	103 - 113
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 114 through 128 )	L	114 - 128
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 150 )	L	129 - 150
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 151 through 163 )	L	151 - 163
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 164 through 174 )	L	164 - 174
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 175 through 188 )	L	175 - 188
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 189 through 214 )	L	189 - 214
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1 through 104 )	A	1 - 104
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 105 through 139 )	A	105 - 139
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 140 through 160 )	A	140 - 160
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 161 through 230 )	A	161 - 230
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 1 through 102 )	B	1 - 102
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 103 through 128 )	B	103 - 128
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 129 through 150 )	B	129 - 150
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 151 through 163 )	B	151 - 163
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 164 through 188 )	B	164 - 188
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 189 through 214 )	B	189 - 214

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi