PDB-4kte: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE1...

ID or keywords:

Entry

Database: PDB / ID: 4kte

Title

Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE148, from non-human primate

Components

GE148 Heavy Chain Fab
GE148 Light Chain Fab

Keywords

IMMUNE SYSTEM / Antibody Affinity / Antibody Specificity / Vaccine Elicited Antibodies /

Fab fragment /

AIDS Vaccines

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Macaca mulatta (Rhesus monkey)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Poulsen, C. / Tran, K. / Stanfield, R. / Wyatt, R.T.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.
Authors: Tran, K. / Poulsen, C. / Guenaga, J. / de Val Alda, N. / Wilson, R. / Sundling, C. / Li, Y. / Stanfield, R.L. / Wilson, I.A. / Ward, A.B. / Karlsson Hedestam, G.B. / Wyatt, R.T.

History

Deposition	May 20, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4kte.cif.gz	185.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4kte.ent.gz	152.8 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/4kte ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kte	HTTPS FTP

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Related structure data

Related structure data	4ktdC C: citing same article (ref.)
Similar structure data	1rz8-1 6e65-d 5mvj-4 6mfj-1 5mp5-4 6dca-2 1mjj-1 6med-1 1a3l-d 5mp1-2 6z3k-8 6qna-4 6wwc-2 3g6j-4 7c95-2 5mv4-8 4z0b-d 6z3k-6 6rlm-4 3l7f-3 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

H: GE148 Heavy Chain Fab

L: GE148 Light Chain Fab

hetero molecules

48.8 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)	42.710, 72.040, 175.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	GE148 Heavy Chain Fab Mass: 24822.838 Da / Num. of mol.: 1 / Fragment: Fab fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody	GE148 Light Chain Fab Mass: 23628.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.79 Å³/Da / Density % sol: 55.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.17M NH4SO4, 25.5%(w/v) PEG4000, 15%(v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 1.03317 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2012

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03317 Å / Relative weight: 1

Reflection

Resolution: 1.8→20 Å / Num. all: 51295 / Num. obs: 51192 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 27.458 Å² / R_merge(I) obs: 0.062 / Net I/σ(I): 21.09

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
1.8-1.85	0.497	4.06	28998	3982	1	100
1.85-1.9	0.379	5.29	25962	3566	1	100
1.9-2	0.264	7.44	44716	6128	1	100
2-2.4	0.147	13.03	113966	15601	1	99.9
2.4-2.8	0.081	21.89	58051	7985	1	99.9
2.8-4	0.039	39.93	64351	9046	1	99.7
4-8	0.028	52.92	29265	4257	1	99.4
8-15	0.025	55.16	3560	566	1	99.5
15-20	0.024	51.38	349	61	1	98.4

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.7.2_869	refinement
PDB_EXTRACT	3.11	data extraction
Blu-Ice		data collection
XDS		data reduction
Auto-Rickshaw		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8897 / SU ML: 0.4 / σ(F): 2 / Phase error: 17.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1935	2560	5 %	Random
R_work	0.1647	-	-	-
obs	0.1662	51191	99.85 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.208 Å² / k_sol: 0.389 e/Å³

Displacement parameters

B_iso max: 80.58 Å² / B_iso mean: 25.9475 Å² / B_iso min: 8.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.6899 Å²	0 Å²	-0 Å²
2-	-	5.0094 Å²	0 Å²
3-	-	-	-2.3195 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→19.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3259	0	21	496	3776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3366
X-RAY DIFFRACTION	f_angle_d	1.154	4593
X-RAY DIFFRACTION	f_chiral_restr	0.079	521
X-RAY DIFFRACTION	f_plane_restr	0.005	579
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9	1181

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8346	0.2077	139	0.1886	2647	2786	100
1.8346-1.872	0.2411	140	0.1948	2662	2802	100
1.872-1.9127	0.2452	140	0.1835	2657	2797	100
1.9127-1.9571	0.2307	142	0.1732	2692	2834	100
1.9571-2.006	0.2159	140	0.1605	2662	2802	100
2.006-2.0602	0.2017	140	0.1594	2661	2801	100
2.0602-2.1208	0.2457	141	0.1631	2682	2823	100
2.1208-2.1891	0.1986	141	0.1601	2671	2812	100
2.1891-2.2673	0.1926	142	0.1592	2698	2840	100
2.2673-2.3579	0.1825	140	0.164	2660	2800	100
2.3579-2.465	0.1882	142	0.165	2692	2834	100
2.465-2.5947	0.2015	141	0.1685	2695	2836	100
2.5947-2.7569	0.2326	142	0.1779	2695	2837	100
2.7569-2.9692	0.22	143	0.1686	2720	2863	100
2.9692-3.2668	0.1884	145	0.1698	2749	2894	100
3.2668-3.7368	0.1824	143	0.1571	2713	2856	99
3.7368-4.6978	0.1496	146	0.1372	2777	2923	100
4.6978-19.9414	0.1769	153	0.1811	2898	3051	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	4.5778	-1.9611	-0.9443	1.6948	-0.0856	3.2957	-0.0054	0.2726	0.0598	-0.0466	-0.0118	-0.0219	0.0832	0.0873	-0.0147	0.0883	-0.0167	0	0.0742	-0.0221	0.0699	12.8206	-29.9237	-24.8716
2	3.1255	-0.1437	-0.3514	2.1869	0.2975	2.4236	-0.1767	-0.2075	-0.1269	0.0494	0.0975	-0.1111	0.148	0.1989	0.0805	0.0665	0.0113	0.0025	0.0896	-0.0045	0.0665	18.5987	-28.0906	-13.8152
3	6.3139	-1.3355	-0.8812	2.1924	-0.3108	2.423	-0.2296	0.0012	-0.4357	0.0505	0.1391	0.0301	0.2379	0.0201	0.1002	0.0941	-0.0255	0.0193	0.0852	-0.034	0.0945	12.8015	-32.584	-19.4014
4	0.1678	0.1702	0.7817	0.7564	0.5314	3.7452	-0.2577	0.626	-0.0601	0.0384	0.2693	-0.1749	-0.1345	0.5929	0.0357	0.0952	-0.0086	-0.008	0.1016	-0.0214	0.1323	22.8479	-22.4739	-17.039
5	8.5701	1.7239	6.5118	0.9583	1.2429	4.9513	0.0489	0.051	-0.0587	0.0108	0.0635	0.0758	0.1933	0.0912	-0.123	0.1034	0.0202	-0.0199	0.1237	-0.0246	0.1348	28.6799	-19.2145	-10.3058
6	1.0265	-1.0615	0.7044	1.6399	-0.3429	4.2257	-0.0732	0.0402	0.072	-0.0368	0.0858	0.1215	0.1035	-0.2409	-0.0049	0.0911	-0.0358	0.0054	0.0919	0.0078	0.1082	2.3843	-25.2356	-27.962
7	1.394	-0.0505	-0.225	2.2318	-0.6246	2.2821	0.0556	0.0357	0.2493	-0.1516	0.1866	-0.2872	-0.2727	-0.0121	-0.1651	0.1244	-0.0325	0.0468	0.073	-0.0239	0.1624	3.771	-13.1462	-41.744
8	3.4367	2.1746	-2.7182	5.6497	-4.631	6.7349	0.0619	0.2137	0.166	-0.7082	0.0601	-0.1198	0.4062	0.0719	-0.1043	0.2707	0.0051	0.0377	0.1036	-0.0241	0.1364	6.6159	-19.5003	-47.8529
9	3.0063	0.0803	0.441	2.3874	-0.0344	2.3773	-0.1408	0.0258	0.3264	-0.1193	0.0389	0.0359	-0.2759	0.1388	0.071	0.1299	-0.0315	-0.0437	0.1115	0.007	0.1284	21.9744	-6.6387	-11.5552
10	1.7847	0.3964	0.7831	3.8919	0.9556	3.6501	0.0083	-0.007	0.0027	0.0112	0.0488	0.2299	-0.2556	-0.0923	-0.0415	0.1246	-0.0001	-0.0033	0.0684	0.0161	0.1151	-5.5086	-2.1702	-39.7597

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 2:25 )	H	2 - 25
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 26:74 )	H	26 - 74
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 75:92 )	H	75 - 92
4	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 93:104 )	H	93 - 104
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 105:116 )	H	105 - 116
6	X-RAY DIFFRACTION	6	( CHAIN H AND RESID 117:126 )	H	117 - 126
7	X-RAY DIFFRACTION	7	( CHAIN H AND RESID 134:201 )	H	134 - 201
8	X-RAY DIFFRACTION	8	( CHAIN H AND RESID 202:213 )	H	202 - 213
9	X-RAY DIFFRACTION	9	( CHAIN L AND RESID 2:115 )	L	2 - 115
10	X-RAY DIFFRACTION	10	( CHAIN L AND RESID 116:208 )	L	116 - 208

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