PDB-7jks: Crystal structure of vaccine-elicited broadly neutralizing VRC01-...

ID or keywords:

Entry

Database: PDB / ID: 7jks

Title

Crystal structure of vaccine-elicited broadly neutralizing VRC01-class antibody 2411a in complex with HIV-1 gp120 core

Components

HIV-1 gp120 core
The heavy chain of antibody 2411a
The light chain of antibody 2411a

Keywords

IMMUNE SYSTEM / broadly neutralizing antibody / VRC01-class / vaccine-elicited / HIV-1

Biological species

Human immunodeficiency virus 1

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.45 Å

Authors

Zhou, T. / Chen, X. / Kwong, P.D. / Mascola, J.R.

Citation

Journal: Immunity / Year: 2021
Title: Vaccination induces maturation in a mouse model of diverse unmutated VRC01-class precursors to HIV-neutralizing antibodies with >50% breadth.
Authors: Chen, X. / Zhou, T. / Schmidt, S.D. / Duan, H. / Cheng, C. / Chuang, G.Y. / Gu, Y. / Louder, M.K. / Lin, B.C. / Shen, C.H. / Sheng, Z. / Zheng, M.X. / Doria-Rose, N.A. / Joyce, M.G. / ...

History

Deposition	Jul 28, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 9, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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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Download

PDBx/mmCIF format	7jks.cif.gz	331.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7jks.ent.gz	268.8 KB	Display	PDB format
PDBx/mmJSON format	7jks.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7jks_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	7jks_full_validation.pdf.gz	2.1 MB	Display
Data in XML	7jks_validation.xml.gz	30.6 KB	Display
Data in CIF	7jks_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jk/7jks ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jks	HTTPS FTP

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Related structure data

Related structure data	7jktC 4xvsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mft-2 6p8m-d 4xny-d 5f9w-2 5cd5-d 6oz3-d 5wi9-2 4xnz-2 4rwy-d 5i9q-2 4xnz-3 Search similar-shape structures by Omokage search (details)

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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

G: HIV-1 gp120 core

H: The heavy chain of antibody 2411a

L: The light chain of antibody 2411a

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	108.920, 188.330, 45.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

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Antibody , 2 types, 2 molecules HL

#2: Antibody	The heavy chain of antibody 2411a Mass: 25487.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody	The light chain of antibody 2411a Mass: 23543.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 13 molecules G

#1: Protein	HIV-1 gp120 core Mass: 41837.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O

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Sugars , 2 types, 8 molecules

#4: Polysaccharide

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

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}	LINUCS	PDB-CARE

#5: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Details

Has ligand of interest	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: 2.59 Å³/Da / Density % sol: 52.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12 % PEG3350, 100 mM MgCl2, 2 M NaCl and 100 mM Imidazole, pH 6.5. 15 % 2R,3R-butanediol as cryoprotectant

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.419→50 Å / Num. obs: 12487 / % possible obs: 91.9 % / Redundancy: 3.8 % / R_merge(I) obs: 0.123 / R_pim(I) all: 0.065 / R_rim(I) all: 0.14 / Χ²: 1.293 / Net I/σ(I): 6.4

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
3.45-3.51	3.3	0.732	503	0.798	0.397	0.839	0.52	75.9
3.51-3.57	3.4	0.685	510	0.839	0.369	0.783	0.475	76.2
3.57-3.64	3.3	0.622	540	0.848	0.34	0.712	0.536	81.1
3.64-3.72	3.4	0.581	565	0.859	0.326	0.67	0.568	86
3.72-3.8	3.6	0.448	560	0.92	0.236	0.509	0.575	85.8
3.8-3.89	3.8	0.436	599	0.955	0.214	0.488	0.619	88.9
3.89-3.98	3.9	0.33	628	0.982	0.163	0.37	0.614	94.9
3.98-4.09	4	0.275	629	0.976	0.134	0.308	0.759	95.6
4.09-4.21	4	0.223	624	0.987	0.109	0.25	0.875	92
4.21-4.35	4.1	0.197	636	0.992	0.096	0.22	0.991	96.2
4.35-4.5	4	0.189	664	0.989	0.092	0.211	1.215	99.4
4.5-4.68	4	0.14	666	0.996	0.068	0.157	1.267	96.9
4.68-4.89	4.1	0.169	648	0.991	0.084	0.189	1.585	99.2
4.89-5.15	3.9	0.158	686	0.992	0.08	0.178	1.454	99
5.15-5.47	3.7	0.122	671	0.993	0.066	0.14	1.668	99.4
5.47-5.9	4	0.113	674	0.993	0.057	0.128	1.529	96.8
5.9-6.49	4.3	0.092	678	0.997	0.046	0.103	1.646	99.7
6.49-7.43	4.2	0.08	684	0.995	0.04	0.09	1.882	97.6
7.43-9.35	3.7	0.057	657	0.995	0.032	0.066	2.521	90.9
9.35-50	3	0.056	665	0.995	0.036	0.067	3.938	85.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.14-3260-000	refinement
HKL-2000		data reduction
PHASER		phasing
PDB_EXTRACT	3.25	data extraction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XVS

4xvs

Resolution: 3.45→42.298 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3317	584	5.14 %
R_work	0.2828	10783	-
obs	0.2852	11367	84.41 %

Solvent computation

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

Displacement parameters

B_iso max: 258.6 Å² / B_iso mean: 95.7409 Å² / B_iso min: 20.7 Å²

Refinement step

Cycle: final / Resolution: 3.45→42.298 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6011	0	137	12	6160
B_iso mean	-	-	73.65	41.15	-
Num. residues	-	-	-	-	769

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 (%)
3.45-3.7632	0.3948	109	0.3269	1640	53
3.7632-4.3073	0.3284	154	0.2896	2849	91
4.3073-5.425	0.3356	171	0.2741	3124	99
5.425-42.298	0.3105	150	0.275	3170	94

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	0.3553	0.075	0.0728	0.0208	0.0148	-0.0041	-0.0903	-0.2776	0.875	0.2514	0.1439	-0.0506	-0.2405	0.0006	0.1898	0.1589	0.6069	0.089	-0.3228	-0.6196	1.3867	7.0296	85.637	26.6855
2	5.276	-0.3635	-1.3229	1.5055	-0.8743	1.4801	0.4071	-0.9133	1.1447	0.5122	0.3873	-0.0903	-0.3965	-0.1268	0.385	0.3601	0.1226	0.0524	0.3854	0.1976	1.7965	12.847	88.7313	25.7876
3	0.0268	-0.0407	0.0466	0.0587	-0.0733	0.0881	0.1119	-0.1379	-0.199	0.0462	-0.0536	-0.3196	-0.035	0.0824	-0.0459	1.0902	-0.2585	-0.4781	0.5799	-0.2316	1.5341	22.8736	107.914	28.7679
4	0.0209	-0.1601	-0.1434	1.1603	1.0313	0.9144	-0.1265	0.6774	0.2395	-0.0015	-0.7482	0.0555	0.5578	0.8095	-0.2649	1.7077	0.0195	-0.3468	1.2145	0.7563	1.6233	46.3982	107.3485	15.9171
5	0.0641	0.1497	0.0785	0.3441	0.1817	0.0957	-0.146	0.5202	0.2705	-1.1752	0.3184	-0.128	-0.3469	-0.4046	0.0287	1.2658	-0.056	-0.3907	0.9084	0.2693	1.0499	29.0568	110.2937	18.5585
6	0.013	0.0089	-0.0146	0.0045	-0.0084	0.0133	0.1766	0.3752	0.0345	-0.2487	-0.223	-0.0834	0.0083	0.0887	-0	1.6168	0.0602	0.0121	1.1674	0.7399	2.0197	34.5515	108.1133	8.7069
7	0.6068	0.4248	-0.205	0.2968	-0.1427	0.0689	-0.0137	-0.1683	-0.2331	-0.1143	-0.0938	-0.0985	0.2399	0.1024	-0.0774	1.8728	0.262	-0.0375	0.6323	0.1929	0.5478	27.6864	102.3739	30.7245
8	0.1199	0.0002	0.3044	-0.0023	0.0006	0.7752	-0.3535	0.8923	-0.0478	-0.6209	0.1273	-0.4314	-0.4134	0.9334	0.0445	2.2862	-0.3278	0.2887	1.2301	0.0519	1.0339	43.4705	106.3414	8.9428
9	0.0481	0.098	-0.0004	0.2114	0.0823	0.169	-0.0496	-0.3434	-0.0907	0.8314	0.4815	0.0449	-0.1726	-0.8656	-0.0691	2.5358	-0.2778	-0.7637	1.6245	0.6774	1.5949	36.6284	117.1368	14.1518
10	0.9813	0.9926	0.3814	1.1443	0.0803	1.4249	0.4195	0.1279	-0.9715	0.2718	-0.2287	-0.1954	0.305	-0.0423	0.0019	0.6422	0.1707	-0.0485	0.4399	0.0028	0.5794	-0.4675	42.557	19.4883
11	3.1626	-0.0579	0.0521	0.9578	0.0849	0.6158	0.3961	1.1649	0.0504	-0.455	-0.4546	0.3721	0.4636	0.1098	-0.0987	0.7179	0.1073	0.0601	0.5103	-0.0863	-0.2789	-4.2821	53.307	10.1009
12	0.3322	0.0976	0.0204	3.0135	0.3695	0.0567	-0.2811	0.3548	-0.0267	-1.5142	0.2881	-0.3552	-0.001	0.4857	-0.0631	1.0711	0.3899	0.4135	1.4777	0.0393	-0.1865	7.6684	57.9443	-1.2276
13	1.3905	0.4315	0.4564	1.8907	-0.4046	2.9473	0.4701	1.1381	0.056	-0.8852	0.149	0.1014	0.1524	0.4203	3.3365	0.8748	0.4459	-0.046	0.8944	0.2196	-0.3895	7.5129	53.38	7.3954
14	2.5197	-1.3788	-1.0925	1.8957	-0.2452	2.1624	0.3624	0.6611	1.1051	-0.1896	-0.0224	-0.7496	-0.4224	0.5174	4.2962	-0.2312	0.9404	0.2185	-0.033	0.4549	0.3151	23.5314	70.6748	18.6691
15	0.6322	0.6656	0.5594	0.7954	0.5702	0.4943	-0.3313	0.5887	0.4274	-0.6495	-0.3667	0.2478	0.3299	0.4978	-0.0817	0.4299	0.2357	0.1479	0.9526	0.0278	0.5915	24.775	67.0861	13.0631
16	1.6864	1.1192	0.7044	0.7556	0.4005	0.8426	-0.5466	0.5051	0.5823	-0.4089	-0.0118	0.0524	-0.1764	0.4021	-0.4317	0.5209	0.0815	0.4501	0.4156	0.4236	1.2389	27.3929	79.5971	18.8389
17	3.0867	1.5105	-2.2895	0.7529	-1.2918	3.3403	0.3512	-0.3125	1.189	0.4093	0.1868	1.084	-0.8879	0.5316	-0.2491	0.5752	-0.2177	0.1703	1.188	0.0483	2.8616	44.7601	111.9317	25.1768
18	0.0761	-0.3855	0.4589	2.0534	-2.4059	4.2703	-0.0504	0.7193	0.3328	0.3036	0.3247	-0.2347	-0.7915	-0.3394	0.1927	0.33	-0.3737	0.0277	0.9423	0.3226	1.555	40.7791	95.4024	24.1749
19	0.1731	0.8536	-0.5588	4.4432	-2.2674	2.7694	-0.1244	-0.3748	1.0178	1.3123	-0.1341	-0.0816	-1.2063	0.2809	0.3433	0.9137	-0.0752	-0.3743	1.6631	-0.407	2.154	42.8634	108.1755	31.1499
20	0.3718	0.4762	0.2083	0.6238	0.314	0.6992	0.1778	-0.1995	0.3748	-0.0931	0.0892	0.1922	-0.7335	0.4044	0.2351	1.1149	-0.3623	0.4003	0.7846	0.3545	2.7413	51.7951	102.1701	28.0567
21	0.1021	-0.2103	-0.0192	0.635	-0.3691	0.8459	-0.003	-0.5859	0.6002	0.4471	0.5294	0.126	-0.3977	0.1174	-0.3839	0.5474	0.1224	0.3139	0.9415	-0.2657	1.9412	9.968	95.512	23.4458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 19 through 75 )	L	19 - 75
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 76 through 102 )	L	76 - 102
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 103 through 115 )	L	103 - 115
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 116 through 136 )	L	116 - 136
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 137 through 150 )	L	137 - 150
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 151 through 163 )	L	151 - 163
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 164 through 174 )	L	164 - 174
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 175 through 186 )	L	175 - 186
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 187 through 210 )	L	187 - 210
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 45 through 215 )	G	45 - 215
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 216 through 327 )	G	216 - 327
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 328 through 395 )	G	328 - 395
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 396 through 493 )	G	396 - 493
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 1 through 59 )	H	1 - 59
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 60 through 82 )	H	60 - 82
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 82A through 124 )	H	82
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 125 through 143 )	H	125 - 143
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 144 through 176 )	H	144 - 176
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 177 through 187 )	H	177 - 187
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 188 through 216 )	H	188 - 216
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 1 through 18 )	L	1 - 18

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Antibody , 2 types, 2 molecules HL

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Protein / Non-polymers , 2 types, 13 molecules G

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Sugars , 2 types, 8 molecules

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Experimental details

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Experiment

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Antibody , 2 types, 2 molecules HL

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Protein / Non-polymers , 2 types, 13 molecules G

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Sugars , 2 types, 8 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

-
Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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