PDB-4evn: Crystal Structure of Fab CR6261 (somatic heavy chain with germlin...

ID or keywords:

Entry

Database: PDB / ID: 4evn

Title

Crystal Structure of Fab CR6261 (somatic heavy chain with germline-reverted light chain)

Components

Fab Heavy ChainFragment antigen-binding
Fab Lambda Light Chain

Keywords

IMMUNE SYSTEM /

Antibody / influenza HA

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: 2.851 Å

Authors

Whittle, J.R.R.

Citation

Journal: Nature / Year: 2012
Title: Structural and genetic basis for development of broadly neutralizing influenza antibodies.
Authors: Lingwood, D. / McTamney, P.M. / Yassine, H.M. / Whittle, J.R. / Guo, X. / Boyington, J.C. / Wei, C.J. / Nabel, G.J.

History

Deposition	Apr 26, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2012	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4evn.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4evn.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4evn.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/ev/4evn ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4evn	HTTPS FTP

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Related structure data

Related structure data	3gbm 3gbn
Similar structure data	5ywf-2 2aj3-3 4h20-d 5wkz-d 1b4j-d 4c83-1 6a0x-1 4why-2 1jgu-d 3g6a-1 4yr6-1 6jc2-d 3mnv-1 6rco-1 4c83-2 5waw-d 5ibu-2 4tuk-d 6vtu-d 6p4y-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

3gbm

3gbn

Similar structure data

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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

A: Fab Heavy Chain

B: Fab Lambda Light Chain

C: Fab Heavy Chain

D: Fab Lambda Light Chain

E: Fab Heavy Chain

F: Fab Lambda Light Chain

G: Fab Heavy Chain

H: Fab Lambda Light Chain

I: Fab Heavy Chain

J: Fab Lambda Light Chain

K: Fab Heavy Chain

L: Fab Lambda Light Chain

M: Fab Heavy Chain

N: Fab Lambda Light Chain

O: Fab Heavy Chain

P: Fab Lambda Light Chain

389 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fab Heavy Chain

B: Fab Lambda Light Chain

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

2

C: Fab Heavy Chain

D: Fab Lambda Light Chain

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

3

E: Fab Heavy Chain

F: Fab Lambda Light Chain

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

4

G: Fab Heavy Chain

H: Fab Lambda Light Chain

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

5

I: Fab Heavy Chain

J: Fab Lambda Light Chain

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

6

K: Fab Heavy Chain

L: Fab Lambda Light Chain

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

7

M: Fab Heavy Chain

N: Fab Lambda Light Chain

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

8

O: Fab Heavy Chain

P: Fab Lambda Light Chain

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

Unit cell

Length a, b, c (Å)	70.110, 159.270, 176.440
Angle α, β, γ (deg.)	90.00, 89.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2

#1: Antibody	Fab Heavy Chain / Fragment antigen-binding Mass: 25778.137 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody	Fab Lambda Light Chain Mass: 22890.355 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM imidazole pH 6.5, 17.5% polyethylene glycol 8,000, and 3% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE
Radiation	Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.85→55.014 Å / Num. all: 88033 / Num. obs: 86892 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / B_iso Wilson estimate: 52.61 Å² / R_sym value: 0.17 / Net I/σ(I): 11.27
Reflection shell	Resolution: 2.85→2.92 Å / % possible all: 97.8

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.851→55.014 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 32.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2928	2022	2.33 %	RANDOM
R_work	0.2299	-	-	-
all	0.2314	86858	-	-
obs	0.2314	86858	96.26 %	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 27.678 Å² / k_sol: 0.269 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.2253 Å²	0 Å²	0.175 Å²
2-	-	10.6365 Å²	-0 Å²
3-	-	-	-2.4112 Å²

Refinement step

Cycle: LAST / Resolution: 2.851→55.014 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25293	0	0	0	25293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	25965
X-RAY DIFFRACTION	f_angle_d	1.232	35486
X-RAY DIFFRACTION	f_dihedral_angle_d	14.856	8988
X-RAY DIFFRACTION	f_chiral_restr	0.077	4088
X-RAY DIFFRACTION	f_plane_restr	0.006	4545

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1676	X-RAY DIFFRACTION	POSITIONAL
1	2	C	1676	X-RAY DIFFRACTION	POSITIONAL	0.058
1	3	E	1676	X-RAY DIFFRACTION	POSITIONAL	0.058
1	4	G	1676	X-RAY DIFFRACTION	POSITIONAL	0.053
1	5	I	1676	X-RAY DIFFRACTION	POSITIONAL	0.053
1	6	K	1676	X-RAY DIFFRACTION	POSITIONAL	0.069
1	7	M	1676	X-RAY DIFFRACTION	POSITIONAL	0.059
1	8	O	1676	X-RAY DIFFRACTION	POSITIONAL	0.06
2	1	A	1405	X-RAY DIFFRACTION	POSITIONAL
2	2	C	1405	X-RAY DIFFRACTION	POSITIONAL	0.063
2	3	E	1405	X-RAY DIFFRACTION	POSITIONAL	0.071
2	4	G	1405	X-RAY DIFFRACTION	POSITIONAL	0.077
2	5	I	1405	X-RAY DIFFRACTION	POSITIONAL	0.085
2	6	K	1405	X-RAY DIFFRACTION	POSITIONAL	0.09
2	7	M	1405	X-RAY DIFFRACTION	POSITIONAL	0.07
2	8	O	1405	X-RAY DIFFRACTION	POSITIONAL	0.055

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 (%)
2.8508-2.9221	0.461	102	0.4189	3971	X-RAY DIFFRACTION	63
2.9221-3.0011	0.4329	139	0.3327	6171	X-RAY DIFFRACTION	98
3.0011-3.0894	0.386	146	0.2872	6149	X-RAY DIFFRACTION	98
3.0894-3.1891	0.327	149	0.2737	6217	X-RAY DIFFRACTION	99
3.1891-3.3031	0.336	149	0.2685	6182	X-RAY DIFFRACTION	99
3.3031-3.4353	0.352	148	0.2686	6178	X-RAY DIFFRACTION	99
3.4353-3.5916	0.3135	148	0.2618	6200	X-RAY DIFFRACTION	99
3.5916-3.7809	0.3334	149	0.2517	6225	X-RAY DIFFRACTION	99
3.7809-4.0177	0.3466	143	0.2553	6195	X-RAY DIFFRACTION	99
4.0177-4.3278	0.3093	148	0.2212	6273	X-RAY DIFFRACTION	99
4.3278-4.7631	0.2632	147	0.1826	6211	X-RAY DIFFRACTION	99
4.7631-5.4519	0.2329	147	0.1879	6260	X-RAY DIFFRACTION	99
5.4519-6.8667	0.2446	152	0.1987	6275	X-RAY DIFFRACTION	99
6.8667-55.0244	0.2158	155	0.1885	6329	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	1.9319	0.466	0.7849	2.021	0.2177	3.0891	0.3708	-0.3946	-0.5027	0.485	0.0957	-0.1307	0.1022	-0.1164	-0.2629	0.5099	-0.1382	-0.2302	0.4471	0.1074	0.2747	-21.2195	-8.8544	47.5731
2	0.6846	-0.2609	-0.0568	1.8549	-0.5092	0.6502	-0.0397	0.018	-0.15	-0.0056	-0.0314	-0.0731	0.1338	0.0782	0.0636	0.051	-0.0039	0.0427	0.0421	0.0516	0.0829	-22.6423	30.8976	2.7537
3	1.2671	0.9215	0.1339	2.4438	0.571	0.4395	0.0099	-0.1951	0.0981	0.2196	0.0342	-0.0171	0.0433	0.0491	-0.018	0.1018	-0.049	0.0869	0.116	-0.0341	0.0461	21.2572	32.6273	32.4397
4	3.0324	0.7263	0.3033	1.7072	0.7376	3.5993	0.5405	0.2446	-0.2922	-0.0842	-0.5989	0.3124	-0.2117	-1.1522	-0.1084	0.493	0.1257	-0.1207	0.9149	-0.1814	0.2781	19.9454	27.9751	67.0507
5	1.3533	0.419	-0.8331	1.4722	0.2327	3.3987	0.1643	0.1263	0.1032	0.0373	-0.1484	-0.0785	-0.165	0.0201	0.0101	0.3365	-0.1204	-0.0953	0.8845	0.2012	0.2437	-20.0377	-2.4048	82.4586
6	2.1704	-0.3639	-0.8441	1.1342	0.4133	1.6993	0.145	0.1818	0.328	-0.2021	-0.0868	0.0446	-0.3069	-0.1668	0.0261	0.0479	0.1542	0.0157	0.0299	0.0044	-0.003	18.3918	-4.4057	-17.5355
7	1.9191	-0.7381	0.5101	2.8183	0.3551	2.2089	0.326	0.4465	-0.2904	-0.7105	-0.4518	0.1635	0.2477	0.1102	0.0975	0.385	0.2444	-0.0018	0.4141	-0.0444	0.1423	-19.3706	24.8044	-32.3224
8	0.5429	-0.1139	0.0706	1.2646	0.2949	0.2596	0.01	-0.0144	-0.0754	0.1184	0.0489	-0.0688	0.0222	0.0187	0.0727	0.0308	0.0634	-0.0086	-0.0226	-0.0685	-0.0175	22.6136	-9.4721	17.8424
9	1.4766	-0.2474	-0.1688	1.4279	0.2665	0.529	0.1362	0.1325	-0.1514	-0.0876	-0.0267	0.0764	-0.0147	0.0419	0.0521	0.0401	0.0316	-0.0021	0.0915	-0.1267	0.1555	-14.2361	-11.0511	11.0373
10	1.2353	-0.6171	-0.3119	2.4901	-0.9858	0.8647	0.0166	-0.4889	0.0757	0.6108	-0.0835	-0.3809	-0.2668	0.2667	-0.0413	0.1543	-0.1255	-0.1488	0.2576	0.0637	0.0714	-15.8585	35.6479	38.9526
11	1.1644	0.0897	0.4433	2.0268	-0.4952	0.5733	-0.0129	0.2221	0.0871	-0.2357	0.0083	0.0518	0.0084	0.0747	-0.0016	0.0394	-0.0015	-0.0269	0.0591	0.0417	0.0254	14.2195	31.9761	-4.296
12	4.3436	-0.0043	-0.3915	1.3688	-0.7096	2.4727	-0.4763	0.2377	0.3262	-0.2935	0.2332	0.3163	-0.1416	-0.1762	0.1239	0.5624	0.1648	-0.2386	0.724	-0.1862	0.3202	18.3923	30.5884	103.3246
13	3.6601	-0.3708	-0.5729	1.056	0.0434	0.9354	-0.0841	0.1231	0.1746	-0.0876	-0.0058	-0.1764	-0.0108	0.1213	-0.0226	0.0802	-0.0651	0.0279	0.3959	0.1706	0.1263	-19.004	-7.3208	118.5713
14	2.9834	1.078	-0.227	2.0425	-0.1975	1.0321	-0.1182	-0.0042	0.1173	0.0604	0.0392	0.3446	0.039	-0.3069	0.009	0.0839	0.0274	0.0645	0.5323	0.068	0.1612	15.9519	-7.7413	-53.4227
15	3.3228	0.696	0.3116	0.341	-0.1016	1.1196	-0.2217	0.016	0.1124	0.0517	0.115	-0.1373	0.1964	0.4375	-0.0538	0.5155	0.3006	-0.2399	0.717	-0.176	0.3663	-18.3363	30.0892	-68.6193
16	0.8388	-0.9142	-0.0345	2.757	-0.3033	1.2086	0.2043	-0.8809	-0.3273	1.1192	-0.0788	0.2886	-0.103	-0.1313	-0.0168	0.7108	-0.3363	0.0516	0.7802	0.1872	0.3389	15.8703	-10.9328	54.4484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:116 ) OR ( CHAIN B AND RESID 3:109 )	A	1 - 116
2	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:116 ) OR ( CHAIN B AND RESID 3:109 )	B	3 - 109
3	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 1:116 ) OR ( CHAIN D AND RESID 3:109 )	C	1 - 116
4	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 1:116 ) OR ( CHAIN D AND RESID 3:109 )	D	3 - 109
5	X-RAY DIFFRACTION	3	( CHAIN E AND RESID 1:116 ) OR ( CHAIN F AND RESID 3:109 )	E	1 - 116
6	X-RAY DIFFRACTION	3	( CHAIN E AND RESID 1:116 ) OR ( CHAIN F AND RESID 3:109 )	F	3 - 109
7	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 3:109 ) OR ( CHAIN G AND RESID 1:116 )	H	3 - 109
8	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 3:109 ) OR ( CHAIN G AND RESID 1:116 )	G	1 - 116
9	X-RAY DIFFRACTION	5	( CHAIN I AND RESID 1:116 ) OR ( CHAIN J AND RESID 3:109 )	I	1 - 116
10	X-RAY DIFFRACTION	5	( CHAIN I AND RESID 1:116 ) OR ( CHAIN J AND RESID 3:109 )	J	3 - 109
11	X-RAY DIFFRACTION	6	( CHAIN K AND RESID 1:116 ) OR ( CHAIN L AND RESID 3:109 )	K	1 - 116
12	X-RAY DIFFRACTION	6	( CHAIN K AND RESID 1:116 ) OR ( CHAIN L AND RESID 3:109 )	L	3 - 109
13	X-RAY DIFFRACTION	7	( CHAIN M AND RESID 1:116 ) OR ( CHAIN N AND RESID 3:109 )	M	1 - 116
14	X-RAY DIFFRACTION	7	( CHAIN M AND RESID 1:116 ) OR ( CHAIN N AND RESID 3:109 )	N	3 - 109
15	X-RAY DIFFRACTION	8	( CHAIN P AND RESID 3:109 ) OR ( CHAIN O AND RESID 1:116 )	P	3 - 109
16	X-RAY DIFFRACTION	8	( CHAIN P AND RESID 3:109 ) OR ( CHAIN O AND RESID 1:116 )	O	1 - 116
17	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 117:228 ) OR ( CHAIN B AND RESID 113:215 )	A	117 - 228
18	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 117:228 ) OR ( CHAIN B AND RESID 113:215 )	B	113 - 215
19	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 117:228 ) OR ( CHAIN D AND RESID 113:215 )	C	117 - 228
20	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 117:228 ) OR ( CHAIN D AND RESID 113:215 )	D	113 - 215
21	X-RAY DIFFRACTION	11	( CHAIN E AND RESID 117:228 ) OR ( CHAIN F AND RESID 113:215 )	E	117 - 228
22	X-RAY DIFFRACTION	11	( CHAIN E AND RESID 117:228 ) OR ( CHAIN F AND RESID 113:215 )	F	113 - 215
23	X-RAY DIFFRACTION	12	( CHAIN H AND RESID 113:215 ) OR ( CHAIN G AND RESID 117:228 )	H	113 - 215
24	X-RAY DIFFRACTION	12	( CHAIN H AND RESID 113:215 ) OR ( CHAIN G AND RESID 117:228 )	G	117 - 228
25	X-RAY DIFFRACTION	13	( CHAIN I AND RESID 117:228 ) OR ( CHAIN J AND RESID 113:215 )	I	117 - 228
26	X-RAY DIFFRACTION	13	( CHAIN I AND RESID 117:228 ) OR ( CHAIN J AND RESID 113:215 )	J	113 - 215
27	X-RAY DIFFRACTION	14	( CHAIN K AND RESID 117:228 ) OR ( CHAIN L AND RESID 113:215 )	K	117 - 228
28	X-RAY DIFFRACTION	14	( CHAIN K AND RESID 117:228 ) OR ( CHAIN L AND RESID 113:215 )	L	113 - 215
29	X-RAY DIFFRACTION	15	( CHAIN M AND RESID 117:228 ) OR ( CHAIN N AND RESID 113:215 )	M	117 - 228
30	X-RAY DIFFRACTION	15	( CHAIN M AND RESID 117:228 ) OR ( CHAIN N AND RESID 113:215 )	N	113 - 215
31	X-RAY DIFFRACTION	16	( CHAIN P AND RESID 113:215 ) OR ( CHAIN O AND RESID 117:228 )	P	113 - 215
32	X-RAY DIFFRACTION	16	( CHAIN P AND RESID 113:215 ) OR ( CHAIN O AND RESID 117:228 )	O	117 - 228

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