PDB-4ris: Structural Analysis of the Unmutated Ancestor of the HIV-1 Envelo...

ID or keywords:

Entry

Database: PDB / ID: 4ris

Title

Structural Analysis of the Unmutated Ancestor of the HIV-1 Envelope V2 Region Antibody CH58 Isolated From an RV144 HIV-1 Vaccine Efficacy Trial Vaccinee and Associated with Decreased Transmission Risk

Components

CH58-UA Fab heavy chain
CH58-UA Fab light chain
Envelope glycoprotein

Keywords

IMMUNE SYSTEM / antibody / IgG fold / HIV-1 gp120 V2 region

Function / homology

Function and homology information

membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Nicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Liao, H.-X. / Alam, S.M. / Hwang, K.-K. / Bonsignori, M. / Rerks-Ngarm, S. ...

Citation

Journal: EBioMedicine / Year: 2015
Title: Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee.
Authors: Nicely, N.I. / Wiehe, K. / Kepler, T.B. / Jaeger, F.H. / Dennison, S.M. / Rerks-Ngarm, S. / Nitayaphan, S. / Pitisuttithum, P. / Kaewkungwal, J. / Robb, M.L. / O'Connell, R.J. / Michael, N.L. ...

History

Deposition	Oct 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 1.2	Nov 27, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ris.cif.gz	193.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ris.ent.gz	155.2 KB	Display	PDB format
PDBx/mmJSON format	4ris.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ris_validation.pdf.gz	443.1 KB	Display	wwPDB validaton report
Full document	4ris_full_validation.pdf.gz	445.8 KB	Display
Data in XML	4ris_validation.xml.gz	19.6 KB	Display
Data in CIF	4ris_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/4ris ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4ris	HTTPS FTP

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Related structure data

Related structure data	4rirC C: citing same article (ref.)
Similar structure data	6fy2-1 6pbw-d 6db7-1 6fy3-2 5wna-1 1u91-d 6fy2-2 2pw1-d 6fy0-1 2p8p-d 3mob-d 4xc1-d 1yeh-d 2egz-d 5iq9-1 5dd0-d 3bky-d 6ws6-1 1q9o-1 1q9o-2 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 (3) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (3) #62 - Feb 2005 Major Histocompatibility Complex similarity (3)

Deposited unit

P: Envelope glycoprotein

H: CH58-UA Fab heavy chain

L: CH58-UA Fab light chain

50.3 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)	55.719, 53.908, 73.573
Angle α, β, γ (deg.)	90.00, 108.92, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein/peptide	Envelope glycoprotein Mass: 2136.538 Da / Num. of mol.: 1 Fragment: HIV-1 gp120 derived peptide (UNP residues 160-177) Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: K7Z4Z0, UniProt: Q70966*PLUS
#2: Antibody	CH58-UA Fab heavy chain Mass: 24949.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#3: Antibody	CH58-UA Fab light chain Mass: 23170.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE PEPTIDE WAS DERIVED FROM THE GP120 V2 REGION SEQUENCE WITH THE TWO NOTED ALANINE RESIDUES AS ...THE PEPTIDE WAS DERIVED FROM THE GP120 V2 REGION SEQUENCE WITH THE TWO NOTED ALANINE RESIDUES AS SUBSTITUTIONS.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: A drop composed of 0.2 ul protein and 0.4 ul well. the well contains 60 ul of 0.2 M calcium acetate hydrate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2013
Radiation	Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 18276 / Num. obs: 18258 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.3→2.34 Å / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→36.918 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 25.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2462	1850	10.13 %	randomized selection
R_work	0.1612	-	-	-
obs	0.1698	18258	96.4 %	-
all	-	18276	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→36.918 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3461	0	0	233	3694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3556
X-RAY DIFFRACTION	f_angle_d	1.136	4836
X-RAY DIFFRACTION	f_dihedral_angle_d	14.523	1264
X-RAY DIFFRACTION	f_chiral_restr	0.073	533
X-RAY DIFFRACTION	f_plane_restr	0.006	612

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 (%)
2.3-2.3459	0.3136	130	0.1933	1068	X-RAY DIFFRACTION	83
2.3459-2.4149	0.2878	138	0.1921	1209	X-RAY DIFFRACTION	94
2.4149-2.4928	0.3323	137	0.201	1212	X-RAY DIFFRACTION	95
2.4928-2.5819	0.3304	146	0.1992	1254	X-RAY DIFFRACTION	95
2.5819-2.6852	0.2743	141	0.1923	1231	X-RAY DIFFRACTION	96
2.6852-2.8074	0.2741	133	0.1951	1279	X-RAY DIFFRACTION	97
2.8074-2.9554	0.3154	145	0.2024	1286	X-RAY DIFFRACTION	98
2.9554-3.1404	0.296	146	0.1819	1263	X-RAY DIFFRACTION	98
3.1404-3.3828	0.273	140	0.1795	1318	X-RAY DIFFRACTION	99
3.3828-3.7229	0.2234	144	0.1703	1290	X-RAY DIFFRACTION	99
3.7229-4.2609	0.2392	144	0.1372	1321	X-RAY DIFFRACTION	100
4.2609-5.3657	0.1906	153	0.1082	1316	X-RAY DIFFRACTION	100
5.3657-36.9225	0.1535	153	0.1278	1361	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	9.7659	-4.185	0.7959	6.5967	1.5188	3.1977	-0.0703	0.8096	0.8954	-0.5801	-0.0111	-0.3813	-0.4478	0.2752	0.1416	0.3111	-0.0643	0.0013	0.2143	0.074	0.1972	44.2081	-105.2746	84.9128
2	4.3098	2.0073	1.2974	1.4075	1.3528	2.4318	0.2257	-0.2938	0.6652	0.1922	0.0951	-0.3584	-0.1711	0.3493	-0.1556	0.1579	-0.0641	0.0245	0.432	-0.0114	0.2181	54.2957	-107.8936	94.6925
3	2.3572	0.2778	-0.3537	2.9611	0.7349	2.4686	0.1844	-0.4384	0.3546	0.2776	-0.0834	-0.0068	-0.2001	0.1635	-0.0861	0.1928	-0.089	0.0449	0.2578	-0.0294	0.2427	40.3677	-107.3518	97.6664
4	2.4533	-1.3081	-0.5616	3.147	0.4552	1.121	-0.1105	-0.2032	0.0373	0.2231	0.0015	-0.2416	0.0856	0.3592	0.1068	0.2156	0.0026	-0.005	0.2758	-0.0129	0.111	47.2147	-113.1818	95.4693
5	3.7035	1.1006	-0.8246	3.485	3.7646	5.2766	0.0006	-0.0721	0.7707	0.0381	-0.222	0.5428	-0.4349	-0.6096	0.2479	0.3433	0.1176	0.0872	0.1967	-0.022	0.3769	19.5336	-104.6303	94.682
6	3.8835	-2.0923	-0.829	1.2318	0.4996	0.2299	0.128	-0.0001	0.2583	-0.1447	-0.0624	-0.0954	-0.1479	-0.0113	-0.0728	0.2326	-0.0006	0.0055	0.1348	0.0154	0.1992	53.2285	-118.8183	86.3786
7	1.0172	0.7113	2.2362	2.1503	0.1002	6.3137	0.1946	-0.0521	-0.3612	0.1712	0.1444	-0.5862	0.3082	0.1488	-0.2987	0.6804	-0.2003	-0.3287	0.4739	-0.3433	1.0489	68.9069	-150.6781	66.9665
8	0.5612	-0.2899	0.0612	4.138	1.7163	1.5235	-0.1562	0.1423	0.1077	-0.2309	0.0237	0.5046	-0.0969	-0.0123	0.0898	0.2539	-0.035	-0.0352	0.2073	0.0376	0.2387	63.9095	-130.0515	73.136
9	1.3942	0.9416	0.7252	4.6274	3.4177	3.3184	-0.1196	0.0864	0.0678	-0.0694	0.1233	0.249	0.2428	0.1354	0.02	0.1657	0.0143	-0.0419	0.1872	0.0832	0.2211	65.0235	-132.3033	74.4425
10	3.7406	-1.9697	-0.892	4.3632	3.9908	5.1375	0.0318	0.3286	0.2967	-0.3235	0.0235	-0.2597	0.0184	0.0921	-0.067	0.1337	-0.0548	0.0009	0.1679	0.0279	0.1375	72.6511	-128.6265	73.624
11	0.3911	0.1	-0.2039	1.7709	0.7495	0.6226	0.0419	-0.2088	0.0299	0.4194	-0.2291	-0.1542	-0.0251	0.1909	0.043	0.5082	-0.2243	0.0122	0.1949	0.2484	0.1734	31.9601	-127.6815	102.9644
12	2.175	-0.0129	0.7372	2.2371	0.0974	4.1005	0.1236	-0.0109	-0.0655	-0.0083	0.0358	0.0109	0.0457	-0.1564	-0.1302	0.11	0.0092	0.0267	0.1277	-0.0009	0.1809	26.9119	-124.8177	88.7382
13	2.8751	0.3728	1.0347	3.2862	2.7499	3.9573	-0.019	0.3124	0.0851	0.0492	0.0743	-0.2284	-0.0148	0.2162	-0.1072	0.1486	-0.0152	0.0405	0.1472	0.035	0.165	30.401	-126.0872	83.0804
14	3.9495	-3.5658	-3.1473	7.087	4.951	3.6618	-0.0216	-0.7532	0.1237	1.0589	0.0091	-0.0469	0.6572	0.5266	0.0532	0.2579	-0.0138	-0.0101	0.253	-0.0127	0.1914	31.8615	-117.9434	101.7528
15	4.3196	-2.0611	-0.7819	1.7716	-0.0117	0.3663	0.1427	0.2689	-0.4617	-0.3858	-0.0422	0.3352	-0.1019	0.1159	-0.1634	0.2631	-0.0392	0.0064	0.231	-0.0686	0.2409	39.9049	-136.7469	78.0348
16	5.6805	-0.2377	0.1286	0.862	0.3136	0.3813	-0.05	-0.1193	-0.4758	0.0156	0.0069	0.1106	0.074	-0.1673	0.0158	0.2141	-0.0345	-0.0028	0.1939	0.0164	0.1924	60.9616	-141.6356	82.9531
17	9.2749	7.0211	-4.6448	6.2549	-1.6463	9.2248	0.2211	-0.8356	-0.4279	1.3036	-0.5091	0.1704	-0.2686	-0.1477	0.0714	0.3644	-0.0526	0.0798	0.4803	0.1364	0.3057	57.6964	-141.3417	93.4102
18	6.157	-0.8803	1.2268	4.5598	0.6476	2.3455	-0.2547	0.6422	0.8177	-0.2803	-0.1678	0.0655	-0.4907	-0.1984	0.4269	0.1966	-0.0165	0.0762	0.3246	0.0417	0.2309	52.6464	-134.6203	78.9687
19	0.3345	0.1142	0.2793	0.2528	-0.4274	1.5221	0.0383	-0.0345	-0.155	0.2022	-0.0766	-0.2657	0.2609	0.273	-0.1841	0.3593	0.1676	-0.0774	0.3818	0.2878	0.4562	70.974	-146.8477	91.6985
20	2.4713	0.1529	-2.5235	2.5003	1.3452	5.0287	0.1488	0.087	-1.1901	0.4636	-0.0974	-0.2842	0.3776	-0.0458	-0.07	0.2989	-0.0577	-0.0377	0.1967	0.0342	0.5	56.4493	-149.2223	82.8367
21	5.5599	0.5895	-4.0649	5.3991	-4.3157	9.4178	0.2955	0.2806	0.2975	0.3275	0.287	2.7338	0.2702	-2.5586	-0.4215	0.3555	-0.1471	0.066	0.4691	0.0789	0.5394	17.1044	-113.4549	101.6621
22	4.373	3.3758	0.4728	6.1113	-0.8573	3.2764	0.0323	-0.3292	0.6745	-0.0714	-0.3281	-0.2076	0.2382	0.2268	0.2188	0.2781	0.0836	0.0904	0.2629	0.0076	0.2572	24.6913	-106.3044	101.3449

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain H and resid 1:10)
2	X-RAY DIFFRACTION	2	(chain H and resid 11:24)
3	X-RAY DIFFRACTION	3	(chain H and resid 25:81)
4	X-RAY DIFFRACTION	4	(chain H and resid 82:96)
5	X-RAY DIFFRACTION	5	(chain H and resid 97:100F)
6	X-RAY DIFFRACTION	6	(chain H and resid 100G:126)
7	X-RAY DIFFRACTION	7	(chain H and resid 127:132)
8	X-RAY DIFFRACTION	8	(chain H and resid 133:164)
9	X-RAY DIFFRACTION	9	(chain H and resid 165:200)
10	X-RAY DIFFRACTION	10	(chain H and resid 201:215)
11	X-RAY DIFFRACTION	11	(chain L and resid 1:5)
12	X-RAY DIFFRACTION	12	(chain L and resid 6:71)
13	X-RAY DIFFRACTION	13	(chain L and resid 72:90)
14	X-RAY DIFFRACTION	14	(chain L and resid 91:98)
15	X-RAY DIFFRACTION	15	(chain L and resid 99:115)
16	X-RAY DIFFRACTION	16	(chain L and resid 116:153)
17	X-RAY DIFFRACTION	17	(chain L and resid 154:160)
18	X-RAY DIFFRACTION	18	(chain L and resid 161:180)
19	X-RAY DIFFRACTION	19	(chain L and resid 181:188)
20	X-RAY DIFFRACTION	20	(chain L and resid 189:209)
21	X-RAY DIFFRACTION	21	(chain P and resid 166:170)
22	X-RAY DIFFRACTION	22	(chain P and resid 171:179)

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