PDB-4k3d: Crystal structure of bovine antibody BLV1H12 with ultralong CDR H3

ID or keywords:

Entry

Database: PDB / ID: 4k3d

Title

Crystal structure of bovine antibody BLV1H12 with ultralong CDR H3

Components

BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN

Keywords

IMMUNE SYSTEM /

IMMUNOGLOBULIN /

CYSTINE KNOT /

IMMUNE RECOGNITION

Function / homology

Function and homology information

Immunoglobulin V-Type /

Immunoglobulin V-set domain /

Immunoglobulin V-set domain / Immunoglobulin subtype /

Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set /

Immunoglobulin C1-set domain ...
Similarity search - Domain/homology

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Ekiert, D.C. / Wang, F. / Wilson, I.A.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2013
Title: Reshaping antibody diversity.
Authors: Wang, F. / Ekiert, D.C. / Ahmad, I. / Yu, W. / Zhang, Y. / Bazirgan, O. / Torkamani, A. / Raudsepp, T. / Mwangi, W. / Criscitiello, M.F. / Wilson, I.A. / Schultz, P.G. / Smider, V.V.

History

Deposition	Apr 10, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Database references
Revision 2.0	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4k3d.cif.gz	382.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4k3d.ent.gz	313.3 KB	Display	PDB format
PDBx/mmJSON format	4k3d.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/k3/4k3d ftp://data.pdbj.org/pub/pdb/validation_reports/k3/4k3d	HTTPS FTP

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Related structure data

Related structure data	4k3eC 1bvkS 2fb4S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6e9h-d 4k3e-2 6e8v-2 7lsg-d 6k7o-3 6w0e-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

H: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN

L: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN

I: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN

M: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN

hetero molecules

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

1

H: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN

L: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN

hetero molecules

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

2

I: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN

M: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN

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

Unit cell

Length a, b, c (Å)	71.410, 127.600, 127.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN Mass: 29791.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: IGH / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody	BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN / IGL@ protein Mass: 22531.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: IGL, IGL@ / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3T101
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	DUE TO THE UNUSUAL LENGTH OF THE CDR H3 LOOP, ADDITIONAL CDR H3 RESIDUES BEYOND KABAT POSITION 100Z ...DUE TO THE UNUSUAL LENGTH OF THE CDR H3 LOOP, ADDITIONAL CDR H3 RESIDUES BEYOND KABAT POSITION 100Z WERE ACCOMMODATED AT POSITIONS 101 AND 102. THESE SEQUENCES REFER TO ANTIBODY CHAINS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.81 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.27 M potassium citrate and 22% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2010
Radiation	Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 100271 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / B_iso Wilson estimate: 31.9 Å² / R_sym value: 0.09 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.85→1.94 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.5 / R_sym value: 0.73 / % possible all: 92.3

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
XPREP		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BVK and 2FB4

1bvk

2fb4

Resolution: 1.85→40.427 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 24.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2104	4921	5.01 %	RANDOM
R_work	0.1823	-	-	-
obs	0.1838	98233	97.98 %	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→40.427 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6700	0	14	747	7461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7273
X-RAY DIFFRACTION	f_angle_d	1.139	9970
X-RAY DIFFRACTION	f_dihedral_angle_d	12.163	2585
X-RAY DIFFRACTION	f_chiral_restr	0.063	1173
X-RAY DIFFRACTION	f_plane_restr	0.005	1288

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 (%)
1.85-1.871	0.4094	152	0.3671	2813	X-RAY DIFFRACTION	90
1.871-1.893	0.3798	160	0.3435	2950	X-RAY DIFFRACTION	95
1.893-1.9161	0.316	159	0.3178	3058	X-RAY DIFFRACTION	97
1.9161-1.9404	0.3169	166	0.2941	3083	X-RAY DIFFRACTION	98
1.9404-1.9659	0.3108	157	0.2806	3069	X-RAY DIFFRACTION	98
1.9659-1.9928	0.3081	168	0.2828	3083	X-RAY DIFFRACTION	98
1.9928-2.0213	0.2974	174	0.3162	3019	X-RAY DIFFRACTION	97
2.0213-2.0515	0.3244	152	0.2964	3052	X-RAY DIFFRACTION	97
2.0515-2.0835	0.2688	149	0.2471	3088	X-RAY DIFFRACTION	98
2.0835-2.1177	0.293	162	0.2295	3100	X-RAY DIFFRACTION	98
2.1177-2.1542	0.2571	172	0.2222	3107	X-RAY DIFFRACTION	98
2.1542-2.1934	0.2683	154	0.2115	3066	X-RAY DIFFRACTION	98
2.1934-2.2356	0.224	154	0.2059	3106	X-RAY DIFFRACTION	98
2.2356-2.2812	0.2643	174	0.2005	3090	X-RAY DIFFRACTION	98
2.2812-2.3308	0.2673	171	0.1971	3080	X-RAY DIFFRACTION	98
2.3308-2.385	0.2185	149	0.1881	3105	X-RAY DIFFRACTION	99
2.385-2.4446	0.2416	146	0.19	3133	X-RAY DIFFRACTION	99
2.4446-2.5107	0.2287	167	0.1922	3126	X-RAY DIFFRACTION	99
2.5107-2.5846	0.2054	143	0.194	3161	X-RAY DIFFRACTION	99
2.5846-2.668	0.265	144	0.196	3203	X-RAY DIFFRACTION	100
2.668-2.7633	0.2285	187	0.1906	3143	X-RAY DIFFRACTION	100
2.7633-2.8739	0.2253	161	0.1927	3184	X-RAY DIFFRACTION	100
2.8739-3.0047	0.2384	180	0.1901	3173	X-RAY DIFFRACTION	100
3.0047-3.1631	0.2022	163	0.1854	3175	X-RAY DIFFRACTION	100
3.1631-3.3611	0.2008	183	0.1806	3209	X-RAY DIFFRACTION	100
3.3611-3.6205	0.1823	164	0.1645	3187	X-RAY DIFFRACTION	100
3.6205-3.9846	0.1774	178	0.1483	3223	X-RAY DIFFRACTION	100
3.9846-4.5605	0.14	168	0.1243	3246	X-RAY DIFFRACTION	100
4.5605-5.7431	0.1473	168	0.1244	3248	X-RAY DIFFRACTION	100
5.7431-40.4371	0.2079	196	0.1918	3032	X-RAY DIFFRACTION	89

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	1.6836	-0.5402	-0.2686	1.4212	0.966	1.3777	-0.0428	-0.1016	-0.019	0.2588	0.1514	-0.1404	0.1727	0.2639	-0	0.409	-0.0218	-0.0943	0.2724	-0.0257	0.2933	8.7113	-14.842	30.5299
2	-0.2864	-0.3079	0.0979	-0.136	0.5694	0.7258	-0.1502	-0.1196	-0.0325	0.1632	0.0551	0.1522	0.1541	-0.1106	0	0.7057	-0.0392	0.075	0.5233	-0.0562	0.4818	-6.4808	1.069	60.8532
3	0.8831	0.0115	-0.133	0.5972	0.6418	1.3367	-0.0112	0.1743	0.0025	0.1817	0.0767	-0.1133	0.034	0.0501	0.0117	0.3373	0.0051	-0.0293	0.3093	-0.024	0.268	-0.1423	-21.4396	17.9806
4	2.0218	1.0219	-1.025	1.2281	-0.7175	1.5653	-0.0509	0.3517	0.2114	0.0961	0.2784	-0.0408	-0.0088	-0.0981	0.0251	0.2534	0.045	0.0219	0.418	-0.0362	0.3066	-0.8135	-26.445	0.501
5	1.0322	-0.5428	-0.7677	0.5159	0.024	0.909	-0.061	-0.1126	-0.2179	0.2867	-0.0654	0.3739	0.064	-0.1764	-0.0002	0.5325	-0.002	0.058	0.3043	-0.0268	0.4216	-18.9308	-12.9282	34.4915
6	3.067	-0.1123	0.0702	1.8082	0.1969	1.0073	-0.1831	0.0577	0.0644	-0.029	0.0386	0.0774	-0.2288	-0.0861	0	0.4403	0.0007	-0.0154	0.2034	-0.0433	0.3041	-13.3826	-7.3961	30.4894
7	0.1979	0.9046	0.4115	1.3529	0.9402	0.6435	-0.1394	0.1657	0.0394	0.1548	0.0355	0.0783	0.116	0.0724	-0.0007	0.2767	0.0461	-0.0154	0.3099	-0.0489	0.306	-12.6653	-28.0257	11.1208
8	2.8112	0.7582	-0.3406	0.6742	0.92	1.3364	-0.1513	-0.0836	-0.296	0.0266	0.1031	-0.0427	0.0759	0.0502	0.0002	0.2471	0.0204	-0.0008	0.278	-0.0369	0.3011	-13.5207	-38.4585	6.4031
9	0.6473	-1.0621	-0.5395	0.8277	0.2928	0.0569	0.0888	-0.0558	0.0538	-0.0079	-0.0233	-0.0118	0.1632	0.2445	-0	0.46	0.0476	0.0008	0.3481	0.0829	0.3804	-12.8014	-46.12	38.0407
10	0.6451	0.7355	0.2273	0.9098	0.5675	1.837	0.0836	0.0588	0.0681	-0.1489	-0.0008	0.0126	-0.0454	0.198	-0.0001	0.3635	0.0909	0.0495	0.3187	0.0971	0.3395	-14.6846	-42.4066	30.3569
11	1.1707	0.7988	-0.826	0.6824	-0.3243	0.4993	-0.0361	-0.0485	-0.2511	-0.05	-0.1669	-0.1413	0.3272	-0.0338	-0.0002	0.4389	0.0811	0.0449	0.2373	0.0505	0.3646	-23.0107	-52.2936	26.7025
12	0.2875	-0.8121	0.0941	1.5801	-0.1828	1.4083	-0.0815	-0.2834	-0.0102	-0.2002	0.0643	0.0421	-0.1819	0.0301	0.0013	0.2354	-0.0729	0.0294	0.4621	0.0306	0.3518	-23.4127	-32.0303	57.5667
13	1.6361	-0.7629	0.286	0.8028	0.6358	0.7308	-0.0008	-0.0295	-0.3217	-0.2913	0.0779	0.2507	0.0666	-0.2129	0.0001	0.3783	-0.1087	-0.013	0.4442	0.06	0.4819	-26.371	-36.3602	56.9752
14	0.4923	0.3007	0.5717	0.8595	0.7472	0.9309	0.1211	-0.4137	-0.2081	0.061	0.1224	0.1046	0.1442	-0.0184	-0.0001	0.2745	-0.0381	0.0317	0.5753	0.1348	0.4427	-25.0597	-37.4106	66.0235
15	3.6	0.8684	-1.7664	1.8579	-0.1328	0.9295	-0.0024	0.3331	0.1253	-0.1014	0.1549	0.2432	0.3915	-0.4269	0.001	0.3812	-0.0264	-0.0107	0.4422	0.0746	0.3828	-38.6596	-49.2385	29.2456
16	0.9949	-0.4727	-0.1187	0.7747	1.1006	1.9057	-0.0053	0.0049	0.0028	-0.0822	-0.2279	0.1104	-0.0562	-0.1825	0.0001	0.2991	-0.0083	0.0344	0.3555	0.0748	0.3989	-36.0317	-39.1352	43.7388
17	4.3969	-0.0537	-0.2739	0.4067	0.5467	0.5309	-0.0803	0.3277	0.3979	0.036	0.0564	0.1322	-0.1322	-0.0063	0.0094	0.2837	-0.0068	-0.0235	0.4675	0.0465	0.4188	-38.403	-24.0855	59.2044

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 through 87 )	H	2 - 87
2	X-RAY DIFFRACTION	2	chain 'H' and ( resid 88 through 101P )	H	88 - 101
3	X-RAY DIFFRACTION	3	chain 'H' and ( resid 101Q through 145 )	H	101 - 145
4	X-RAY DIFFRACTION	4	chain 'H' and ( resid 146 through 213 )	H	146 - 213
5	X-RAY DIFFRACTION	5	chain 'L' and ( resid 2 through 33 )	L	2 - 33
6	X-RAY DIFFRACTION	6	chain 'L' and ( resid 34 through 95B )	L	34 - 95
7	X-RAY DIFFRACTION	7	chain 'L' and ( resid 96 through 128 )	L	96 - 128
8	X-RAY DIFFRACTION	8	chain 'L' and ( resid 129 through 212 )	L	129 - 212
9	X-RAY DIFFRACTION	9	chain 'I' and ( resid 2 through 32 )	I	2 - 32
10	X-RAY DIFFRACTION	10	chain 'I' and ( resid 33 through 87 )	I	33 - 87
11	X-RAY DIFFRACTION	11	chain 'I' and ( resid 88 through 103 )	I	88 - 103
12	X-RAY DIFFRACTION	12	chain 'I' and ( resid 104 through 145 )	I	104 - 145
13	X-RAY DIFFRACTION	13	chain 'I' and ( resid 146 through 175 )	I	146 - 175
14	X-RAY DIFFRACTION	14	chain 'I' and ( resid 176 through 213 )	I	176 - 213
15	X-RAY DIFFRACTION	15	chain 'M' and ( resid 3 through 75 )	M	3 - 75
16	X-RAY DIFFRACTION	16	chain 'M' and ( resid 76 through 128 )	M	76 - 128
17	X-RAY DIFFRACTION	17	chain 'M' and ( resid 129 through 211 )	M	129 - 211

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Yorodumi