PDB-5tf1: Structure of chimeric 02-CC Fab, a VRC01-like germline antibody

ID or keywords:

Entry

Database: PDB / ID: 5tf1

Title

Structure of chimeric 02-CC Fab, a VRC01-like germline antibody

Components

02-CC Fab Heavy chain
O2-CC Fab Light Chain

Keywords

IMMUNE SYSTEM / Fab / germline / VRC01-like / CD4-BS / HIV-1 / CDRH3

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.858 Å

Authors

Pancera, M.

Funding support

United States, 1items

Citation

Journal: Cell Rep / Year: 2016
Title: Differences in Allelic Frequency and CDRH3 Region Limit the Engagement of HIV Env Immunogens by Putative VRC01 Neutralizing Antibody Precursors.
Authors: Yacoob, C. / Pancera, M. / Vigdorovich, V. / Oliver, B.G. / Glenn, J.A. / Feng, J. / Sather, D.N. / McGuire, A.T. / Stamatatos, L.

History

Deposition	Sep 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5tf1.cif.gz	245.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5tf1.ent.gz	210.8 KB	Display	PDB format
PDBx/mmJSON format	5tf1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tf1_validation.pdf.gz	428.1 KB	Display	wwPDB validaton report
Full document	5tf1_full_validation.pdf.gz	428.5 KB	Display
Data in XML	5tf1_validation.xml.gz	18.7 KB	Display
Data in CIF	5tf1_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/5tf1 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/5tf1	HTTPS FTP

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Related structure data

Related structure data	5tfsC 5tgbC C: citing same article (ref.)
Similar structure data	4wht-6 7lka-3 5ihz-2 1dqq-2 3qg6-2 4rnr-2 5aze-d 6ghg-1 5tkj-3 4jdv-2 3g5x-1 6cnr-d 4qf1-1 4hk0-1 5w05-d 5cd3-3 5cd3-2 2c1p-1 4uom-d 5kg9-2 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	#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: 02-CC Fab Heavy chain

L: O2-CC Fab Light Chain

49.4 kDa, 2 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)	44.579, 58.676, 70.408
Angle α, β, γ (deg.)	90.00, 103.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	02-CC Fab Heavy chain Mass: 26364.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	O2-CC Fab Light Chain Mass: 23019.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.81 Å³/Da / Density % sol: 32.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 0.1 M Hepes pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 29, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.858→34.831 Å / Num. obs: 27409 / % possible obs: 91.8 % / Redundancy: 3.4 % / Net I/σ(I): 16.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 1.858→34.831 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2325	1383	5.05 %
R_work	0.21	-	-
obs	0.2112	27363	91.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.858→34.831 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3219	0	0	219	3438

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3320
X-RAY DIFFRACTION	f_angle_d	0.59	4526
X-RAY DIFFRACTION	f_dihedral_angle_d	12.035	1986
X-RAY DIFFRACTION	f_chiral_restr	0.044	502
X-RAY DIFFRACTION	f_plane_restr	0.003	577

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 (%)
1.8576-1.924	0.3899	79	0.3254	1545	X-RAY DIFFRACTION	55
1.924-2.0011	0.3256	93	0.3008	2093	X-RAY DIFFRACTION	74
2.0011-2.0921	0.2879	147	0.2897	2541	X-RAY DIFFRACTION	90
2.0921-2.2024	0.2698	153	0.2588	2750	X-RAY DIFFRACTION	98
2.2024-2.3404	0.2852	127	0.2558	2858	X-RAY DIFFRACTION	100
2.3404-2.521	0.3117	155	0.2529	2803	X-RAY DIFFRACTION	100
2.521-2.7746	0.2643	152	0.247	2849	X-RAY DIFFRACTION	100
2.7746-3.1759	0.2916	169	0.2182	2819	X-RAY DIFFRACTION	100
3.1759-4.0003	0.218	139	0.183	2854	X-RAY DIFFRACTION	100
4.0003-34.8376	0.1599	169	0.1604	2868	X-RAY DIFFRACTION	99

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	3.6042	1.481	0.3912	4.3957	-0.7102	5.9162	0.4714	-0.1813	-0.4853	-0.0734	0.3386	1.0596	0.4831	-0.7028	-0.6237	0.2791	0.0289	-0.0464	0.3761	-0.0328	0.3051	41.7049	-2.1075	165.0878
2	3.628	0.1203	2.0065	2.5268	-0.0604	6.1462	-0.0899	0.0181	0.2127	-0.0543	-0.0302	0.0427	-0.3399	-0.055	0.0857	0.2365	0.0467	-0.067	0.2003	-0.0303	0.1986	51.9045	3.9599	169.3039
3	1.7963	0.6175	1.7955	1.9813	1.1955	2.7519	-0.0811	0.0826	0.113	-0.0618	0.0376	0.1205	-0.2855	-0.1317	0.0238	0.288	0.0109	-0.0643	0.255	0.0292	0.2214	47.424	0.2384	165.3006
4	8.9179	-7.4734	4.033	7.5389	-4.4123	4.8351	0.597	0.5539	-0.0016	-0.9966	-0.2122	-0.3036	0.4171	-0.1354	-0.3341	0.431	-0.008	-0.1155	0.4734	-0.1223	0.394	41.8637	-25.2486	133.8489
5	1.8575	-1.3095	-0.595	7.5253	2.8813	2.8506	0.0356	-0.2052	-0.1119	0.281	-0.1052	0.1039	0.1475	-0.4258	0.1211	0.2994	0.0021	-0.0661	0.387	-0.0375	0.2676	40.885	-22.8044	144.4414
6	0.9426	0.177	-0.6323	2.6394	1.9468	2.006	-0.0246	0.0575	-0.0999	-0.2601	0.0335	-0.0473	0.0146	-0.3658	0.0099	0.4434	0.0057	-0.1452	0.4654	0.0021	0.2742	43.4924	-23.2701	139.7838
7	4.5649	-2.3336	-2.4452	7.8625	5.2947	5.8202	0.0215	0.5787	-0.6666	0.2179	-0.4349	0.9947	0.313	-0.82	0.5724	0.3591	-0.0267	-0.0597	0.5933	-0.0351	0.4284	32.8446	-23.0334	142.9345
8	4.2484	-1.1419	0.1661	5.0605	2.3444	4.364	0.3205	0.3518	-0.0183	-0.7605	-0.1373	-0.2382	0.0591	0.0731	-0.1422	0.221	0.021	-0.0072	0.3107	0.0118	0.2563	70.0953	-14.6371	157.668
9	5.3351	-0.9412	-1.0915	3.3784	0.6041	6.0586	0.15	0.3602	0.7513	0.2099	0.1049	-0.5138	-0.4913	0.7462	-0.1457	0.3627	-0.0594	-0.0854	0.2957	0.0165	0.3544	70.1683	-5.5712	164.8501
10	7.5279	-1.3631	2.4013	2.3727	0.9306	6.7439	0.0234	-0.0544	0.0355	-0.0145	0.1429	0.0637	0.2731	0.0592	-0.1689	0.3149	0.0048	-0.0489	0.1249	0.0356	0.2419	66.7419	-12.6334	169.7591
11	2.7442	-0.6388	1.393	2.1804	2.0432	3.3706	-0.0162	0.021	-0.0436	-0.017	0.2441	-0.2214	0.2238	0.1472	-0.1418	0.3107	0.0186	-0.0983	0.2282	-0.0009	0.2241	64.3831	-11.1786	162.8544
12	1.0529	0.9218	1.0754	1.3097	2.2819	4.7077	-0.0021	0.0553	-0.1888	0.2397	-0.1121	-0.255	0.3759	0.7388	0.0806	0.4689	0.0399	-0.1109	0.3311	-0.0622	0.3691	64.9978	-24.8284	148.5279
13	5.9438	-3.5967	4.2331	4.0197	-2.4844	7.1718	-0.1823	-0.1915	-0.0396	-0.0896	0.1857	0.1076	-0.2868	-0.4143	-0.0086	0.3548	0.0248	-0.0613	0.3111	-0.064	0.2108	50.5551	-18.9294	133.2989
14	5.4216	-0.7191	3.1116	2.087	-0.2745	6.2105	0.0195	0.4323	0.3281	-0.0976	-0.0878	-0.0602	-0.3105	-0.1545	-0.0015	0.3404	0.0244	-0.0905	0.3446	-0.0267	0.2782	53.7982	-17.2883	131.9922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 67 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 68 through 125 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 126 through 141 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 142 through 171 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 172 through 200 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 201 through 213 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 2 through 18 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 19 through 38 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 39 through 75 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 76 through 98 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 99 through 109 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 110 through 146 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 147 through 207 )

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