PDB-3rpi: Crystal Structure of Fab from 3BNC60, Highly Potent anti-HIV Antibody

ID or keywords:

Entry

Database: PDB / ID: 3rpi

Title

Crystal Structure of Fab from 3BNC60, Highly Potent anti-HIV Antibody

Components

Heavy chain from highly potent anti-HIV neutralizing antibody
Light chain from highly potent anti-HIV neutralizing antibody

Keywords

IMMUNE SYSTEM / IgG /

glycosylation

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: 2.648 Å

Authors

Diskin, R. / Bjorkman, P.J.

Citation

Journal: Science / Year: 2011
Title: Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding.
Authors: Scheid, J.F. / Mouquet, H. / Ueberheide, B. / Diskin, R. / Klein, F. / Oliveira, T.Y. / Pietzsch, J. / Fenyo, D. / Abadir, A. / Velinzon, K. / Hurley, A. / Myung, S. / Boulad, F. / Poignard, ...

History

Deposition	Apr 26, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2011	Group: Database references / Structure summary
Revision 1.2	Sep 28, 2011	Group: Database references
Revision 1.3	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / struct_conn / struct_ref_seq / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq.db_align_end Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rpi.cif.gz	337.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3rpi.ent.gz	280 KB	Display	PDB format
PDBx/mmJSON format	3rpi.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/rp/3rpi ftp://data.pdbj.org/pub/pdb/validation_reports/rp/3rpi	HTTPS FTP

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Related structure data

Similar structure data	6vl9-2 5cd3-1 7lka-4 6uum-2 4kkc-2 5aze-d 3f12-2 3qg6-1 5i1l-2 6vrp-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

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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)

Deposited unit

L: Light chain from highly potent anti-HIV neutralizing antibody

H: Heavy chain from highly potent anti-HIV neutralizing antibody

A: Heavy chain from highly potent anti-HIV neutralizing antibody

B: Light chain from highly potent anti-HIV neutralizing antibody

hetero molecules

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

1

L: Light chain from highly potent anti-HIV neutralizing antibody

H: Heavy chain from highly potent anti-HIV neutralizing antibody

hetero molecules

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

2

A: Heavy chain from highly potent anti-HIV neutralizing antibody

B: Light chain from highly potent anti-HIV neutralizing antibody

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.620, 155.680, 74.760
Angle α, β, γ (deg.)	90.00, 110.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3
1	4
2	4

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain H and (resseq 2:71 or resseq 82:136 or resseq 145:221 ) and (not element H) and sidechain
2	1	1	chain A and (resseq 2:71 or resseq 82:136 or resseq 145:221 ) and (not element H) and sidechain
1	1	2	chain L and (resseq 3:94 or resseq 96:133 or resseq 135:205 ) and (not element H) and sidechain
2	1	2	chain B and (resseq 3:94 or resseq 96:133 or resseq 135:205 ) and (not element H) and sidechain
1	1	3	chain H and (resseq 2:71 or resseq 82:136 or resseq 145:221 ) and (not element H) and backbone
2	1	3	chain A and (resseq 2:71 or resseq 82:136 or resseq 145:221 ) and (not element H) and backbone
1	1	4	chain L and (resseq 3:94 or resseq 96:133 or resseq 135:205) and (not element H) and backbone
2	1	4	chain B and (resseq 3:94 or resseq 96:133 or resseq 135:205) and (not element H) and backbone

NCS ensembles :

ID
1
2
3
4

#1: Antibody

Light chain from highly potent anti-HIV neutralizing antibody /

Mass: 23076.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host:

Homo sapiens (human)

#2: Antibody

Heavy chain from highly potent anti-HIV neutralizing antibody

Mass: 24907.723 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host:

Homo sapiens (human)

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

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

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.61 Å³/Da / Density % sol: 65.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 11.7% PEG20000, 0.1 M sodium acetate, pH 5.0, 100 mM potassium/sodium tartrate, 20 mM lithium sulfate, 10 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.648→39.17 Å / Num. all: 39686 / Num. obs: 38111 / % possible obs: 96 % / Observed criterion σ(F): -99 / Observed criterion σ(I): -99 / Redundancy: 5 % / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.65→2.72 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1959 / % possible all: 68.1

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Processing

Software

Name	Version	Classification
Web-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.648→39.17 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 27.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2576	1860	5.02 %	RANDOM
R_work	0.2077	-	-	-
all	0.2102	38111	-	-
obs	0.2102	37086	93.71 %	-

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 59.347 Å² / k_sol: 0.343 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	13.0447 Å²	0 Å²	2.1672 Å²
2-	-	-6.2115 Å²	-0 Å²
3-	-	-	-6.8333 Å²

Refinement step

Cycle: LAST / Resolution: 2.648→39.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6476	0	28	146	6650

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6682
X-RAY DIFFRACTION	f_angle_d	1.309	9086
X-RAY DIFFRACTION	f_dihedral_angle_d	17.77	2378
X-RAY DIFFRACTION	f_chiral_restr	0.084	998
X-RAY DIFFRACTION	f_plane_restr	0.006	1168

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	H	739	X-RAY DIFFRACTION	POSITIONAL
1	2	A	739	X-RAY DIFFRACTION	POSITIONAL	0.116
2	1	L	775	X-RAY DIFFRACTION	POSITIONAL
2	2	B	775	X-RAY DIFFRACTION	POSITIONAL	0.127
3	1	H	808	X-RAY DIFFRACTION	POSITIONAL
3	2	A	808	X-RAY DIFFRACTION	POSITIONAL	0.003
4	1	L	804	X-RAY DIFFRACTION	POSITIONAL
4	2	B	804	X-RAY DIFFRACTION	POSITIONAL	0.007

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 (%)
2.6485-2.7201	0.4826	95	0.3707	1778	X-RAY DIFFRACTION	63
2.7201-2.8001	0.323	142	0.2641	2547	X-RAY DIFFRACTION	88
2.8001-2.8905	0.2565	146	0.2188	2723	X-RAY DIFFRACTION	94
2.8905-2.9937	0.2597	143	0.2207	2722	X-RAY DIFFRACTION	94
2.9937-3.1135	0.2892	144	0.226	2741	X-RAY DIFFRACTION	96
3.1135-3.2552	0.2891	138	0.2165	2793	X-RAY DIFFRACTION	96
3.2552-3.4267	0.2761	157	0.2181	2826	X-RAY DIFFRACTION	98
3.4267-3.6413	0.2548	148	0.1963	2822	X-RAY DIFFRACTION	98
3.6413-3.9222	0.2455	157	0.2013	2840	X-RAY DIFFRACTION	98
3.9222-4.3164	0.2388	148	0.1961	2843	X-RAY DIFFRACTION	98
4.3164-4.94	0.245	142	0.1658	2869	X-RAY DIFFRACTION	98
4.94-6.2198	0.2492	148	0.204	2855	X-RAY DIFFRACTION	98
6.2198-39.1748	0.2288	152	0.2225	2867	X-RAY DIFFRACTION	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	0.1414	-0.2523	-0.0557	0.7165	0.2522	0.1074	-0.0363	-0.2358	0.0012	0.1401	-0.0851	0.2289	0.1506	-0.2433	-0.0911	0.2736	-0.1355	0.0009	0.5772	0.0199	0.0786	-33.0095	45.2084	-25.0437
2	0.1332	0.0043	0.0758	0.3569	0.2132	0.2101	-0.0203	0.0406	-0.0384	-0.2187	-0.0619	0.1013	-0.0742	-0.0012	0.0002	0.173	0.0364	0.0313	0.0803	0.0074	0.1368	-21.844	50.9403	-19.1049
3	0.1081	-0.1396	-0.1514	0.2037	0.1467	0.2929	-0.0092	-0.0892	0.0426	0.1519	-0.0811	0.213	-0.0476	-0.0484	-0.0316	0.2354	0.1486	0.0827	0.3216	-0.0481	0.1409	-33.2136	54.7498	-19.9928
4	0.187	-0.0736	0.2313	0.046	-0.0824	0.2874	0.0772	0.2413	-0.072	-0.0753	-0.0906	-0.025	0.1147	0.0915	-0.1044	0.0324	0.015	-0.0789	0.1739	-0.0298	0.0022	-25.2363	45.7074	-20.8942
5	0.8065	-0.229	-0.3096	0.9285	0.2999	0.1529	0.0914	-0.0377	-0.6798	-0.1998	-0.0553	-0.0822	0.6937	-0.1391	0.076	0.881	0.0318	-0.1003	0.0671	0.0439	0.5313	-22.9626	20.0236	-34.5763
6	0.0139	0.0422	0.0191	0.1277	0.0583	0.0258	0.039	-0.1086	-0.3248	0.0516	0.0069	0.147	0.3292	-0.0928	-0.0312	0.74	-0.0167	0.043	0.2766	0.2415	0.7355	-27.1749	21.1981	-33.3869
7	0.264	-0.3368	-0.0338	0.576	0.1056	0.2719	-0.0682	0.033	-0.0647	0.0246	-0.0974	0.2062	-0.0096	-0.0585	0.0751	1.1016	0.0652	-0.1195	0.3113	0.0442	1.4679	-33.7146	8.2612	-29.0101
8	2.2007	0.192	0.9586	1.0156	0.1405	0.9769	0.138	-0.1133	-0.5188	0.1315	0.2052	-0.0183	0.591	0.0618	0.6018	0.9316	0.1591	0.2956	0.2968	0.0477	0.3698	-22.9948	18.8988	-30.5661
9	0.1255	0.1208	0.0333	0.1158	0.0316	0.009	-0.0297	0.042	0.1081	0.0832	-0.0283	0.2689	0.0824	-0.0849	0.1264	1.3112	-0.145	-0.3185	0.2746	-0.0457	1.6557	-31.3755	11.067	-38.097
10	0.2892	-0.1998	0.1038	0.2516	0.2351	0.82	0.0513	-0.1725	-0.0842	0.0286	0.2061	-0.205	0.1268	0.32	-0.0378	0.3402	0.1314	0.0512	0.3802	0.0818	0.5183	-7.1066	34.2903	-7.5021
11	0.4132	0.1336	-0.2663	0.1766	0.064	0.4936	0.0632	-0.2336	0.0846	-0.0067	0.0522	-0.1	-0.0514	0.2639	0.0911	0.0315	-0.0458	-0.0212	0.1382	0.0034	0.1747	-15.3498	44.0061	-3.2713
12	0.93	-0.6964	0.0076	0.9324	0.2029	1.6054	-0.1906	-0.1694	0.0517	0.1769	-0.2901	-0.1124	0.2467	0.2366	0.2622	0.4054	0.0228	0.031	0.4834	0.1154	0.3928	-12.4649	38.1148	5.2714
13	0.3292	-0.5262	-0.3008	0.9125	0.2344	1.0715	-0.1256	-0.069	0.2046	0.0235	0.0808	-0.0478	0.0242	0.4719	-0.013	0.2368	-0.0251	-0.1046	0.3441	0.1161	0.4252	-8.1371	37.3093	-2.0601
14	0.2981	0.0537	0.0073	0.03	-0.0558	0.2274	0.2002	-0.0536	-0.2115	-0.2026	-0.1184	-0.1088	0.4613	0.5709	-0.0357	0.4632	0.1811	-0.025	0.252	0.0454	0.2449	-14.1143	33.2027	-15.1482
15	0.0525	-0.0574	0.0268	0.1841	-0.0422	0.0554	-0.0308	0.1977	0.1183	-0.0645	0.005	-0.1069	0.0122	0.0295	-0.0981	1.0153	0.3641	0.358	0.0453	0.1892	0.4477	-12.5814	19.3152	-29.6665
16	0.1144	-0.1318	-0.0255	0.3721	-0.0245	0.0386	0.0938	0.156	0.0268	-0.4521	-0.0197	-0.2643	0.0345	0.0215	0.0356	1.2205	0.3104	0.3268	0.4239	0.1224	0.57	-5.1946	15.6308	-35.9851
17	0.5424	-0.1382	-0.0398	0.4557	0.2291	0.5408	0.0485	0.0093	0.2945	-0.1058	0.0226	-0.2858	-0.0336	0.4496	0.0959	0.2114	-0.0424	-0.0108	0.2325	0.0303	0.1383	-7.0956	-21.501	-20.2043
18	1.0812	0.3376	-0.4238	0.4895	0.0321	0.7173	0.4042	-0.4346	0.557	0.4427	0.0636	-0.289	-0.5501	0.8519	0.4421	-0.365	-0.1911	-0.3337	0.1039	-0.0562	-0.1507	-9.6506	-17.0085	-14.7002
19	0.0183	0.0355	-0.0013	0.0648	-0.0178	0.0312	0.0948	-0.2299	0.0169	0.2427	0.0414	-0.0958	-0.0967	-0.0651	0.1983	1.1851	-0.6127	0.1905	-0.1709	-0.1986	0.3193	-23.3553	0.5099	3.565
20	0.0128	0.025	-0.0075	0.0698	-0.0251	0.0069	0.0339	0.146	0.0312	-0.0238	-0.0276	0.117	-0.0338	-0.041	-0.0647	0.0656	0.0897	0.0614	0.593	0.1189	0.1508	-36.3565	-26.6313	-16.9782
21	0.0432	-0.0151	-0.0093	0.0042	-0.0022	0.0184	-0.0492	-0.014	-0.0242	0.0416	0.001	0.1369	-0.0316	-0.0402	-0.0089	-0.1119	-0.1854	-0.1828	0.0184	-0.1375	-0.0366	-24.0474	-32.4161	-14.1918
22	0.0337	0.0003	-0.0392	0.0081	-0.0316	0.2059	-0.0349	0.0141	-0.1008	-0.0595	-0.0056	-0.0049	0.0093	-0.0267	-0.0704	0.1009	-0.0633	0.0718	0.1175	-0.1892	-0.2004	-33.2407	-36.1739	-20.9654
23	0.3062	-0.0093	0.1377	0.3258	0.0626	0.25	-0.0471	0.013	0.1237	-0.0891	0.0123	0.0539	-0.0874	0.0635	-0.0304	0.1133	-0.0389	-0.0007	0.1614	0.0175	0.1048	-27.7599	-27.1619	-15.0381
24	0.7678	-0.2955	0.1985	0.2737	-0.3	1.0876	0.1932	0.0364	0.8226	0.1241	-0.0612	-0.2474	-0.8739	0.0855	0.2587	0.3586	0.005	0.1856	-0.3286	0.1472	0.3599	-34.8888	-1.5304	-3.0871
25	0.0581	0.0623	-0.0257	0.1005	-0.0771	0.064	0.0042	0.0421	0.1549	-0.0289	-0.075	0.0016	-0.1033	0.0287	-0.0563	0.6336	-0.1124	-0.0711	0.0333	0.3052	0.5059	-37.7546	-0.8421	-7.5301
26	0.3826	0.0083	0.0421	0.0063	0.0269	0.2841	0.0771	0.0252	0.2041	0.0027	0.0471	-0.0015	-0.1141	-0.0698	-0.061	0.7853	-0.0738	0.1505	0.1014	0.125	0.1274	-35.0788	-3.7071	-7.5834
27	0.4651	0.1585	0.1659	0.058	0.0522	0.0406	0.1284	-0.012	0.2918	-0.0705	0.3329	0.0143	-0.3298	0.0618	0.4359	0.892	0.0117	0.0165	0.0873	0.0694	1.0069	-39.4489	9.0504	-6.9662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resseq 3:24)
2	X-RAY DIFFRACTION	2	chain 'L' and (resseq 25:57)
3	X-RAY DIFFRACTION	3	chain 'L' and (resseq 58:71)
4	X-RAY DIFFRACTION	4	chain 'L' and (resseq 72:93)
5	X-RAY DIFFRACTION	5	chain 'L' and (resseq 94:120)
6	X-RAY DIFFRACTION	6	chain 'L' and (resseq 121:139)
7	X-RAY DIFFRACTION	7	chain 'L' and (resseq 140:150)
8	X-RAY DIFFRACTION	8	chain 'L' and (resseq 151:179)
9	X-RAY DIFFRACTION	9	chain 'L' and (resseq 180:205)
10	X-RAY DIFFRACTION	10	chain 'H' and (resseq 2:25)
11	X-RAY DIFFRACTION	11	chain 'H' and (resseq 26:61)
12	X-RAY DIFFRACTION	12	chain 'H' and (resseq 62:75)
13	X-RAY DIFFRACTION	13	chain 'H' and (resseq 76:95)
14	X-RAY DIFFRACTION	14	chain 'H' and (resseq 96:145)
15	X-RAY DIFFRACTION	15	chain 'H' and (resseq 146:194)
16	X-RAY DIFFRACTION	16	chain 'H' and (resseq 195:221)
17	X-RAY DIFFRACTION	17	chain 'A' and (resseq 2:67)
18	X-RAY DIFFRACTION	18	chain 'A' and (resseq 68:145)
19	X-RAY DIFFRACTION	19	chain 'A' and (resseq 146:221)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 3:24)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 25:57)
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 58:71)
23	X-RAY DIFFRACTION	23	chain 'B' and (resseq 72:93)
24	X-RAY DIFFRACTION	24	chain 'B' and (resseq 94:120)
25	X-RAY DIFFRACTION	25	chain 'B' and (resseq 121:142)
26	X-RAY DIFFRACTION	26	chain 'B' and (resseq 143:166)
27	X-RAY DIFFRACTION	27	chain 'B' and (resseq 167:205)

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