PDB-6oan: Structure of DBP in complex with human neutralizing antibody 053054

ID or keywords:

Entry

Database: PDB / ID: 6oan

Title

Structure of DBP in complex with human neutralizing antibody 053054

Components

Antibody 053054 single chain variable fragment
Duffy binding surface protein region II

Keywords

CELL INVASION / Plasmodium / vivax / Duffy Binding Protein / DBP / PvDBP / antibody / neutralizing / inhibition / malaria / invasion / blocking / vaccine / structural vaccinology

Function / homology

Function and homology information

host cell surface receptor binding / identical protein binding / membrane
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Urusova, D. / Tolia, N.H.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	Intramural Research Program	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R56 AI080792	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201400018C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI064478	United States

Citation

Journal: Nat Microbiol / Year: 2019
Title: Structural basis for neutralization of Plasmodium vivax by naturally acquired human antibodies that target DBP.
Authors: Urusova, D. / Carias, L. / Huang, Y. / Nicolete, V.C. / Popovici, J. / Roesch, C. / Salinas, N.D. / Witkowski, B. / Ferreira, M.U. / Adams, J.H. / Gross, M.L. / King, C.L. / Tolia, N.H.

History

Deposition	Mar 18, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oan.cif.gz	402.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6oan.ent.gz	333 KB	Display	PDB format
PDBx/mmJSON format	6oan.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/oa/6oan ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oan	HTTPS FTP

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Related structure data

Related structure data	6oaoC 4nuvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6v5p-1 6wa2-1 6wa2-2 6jc3-d 6fzu-d 5x2f-2 6v5n-2 4a22-2 5hr7-2 6p1l-1 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 - FunctionF&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) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

Deposited unit

A: Duffy binding surface protein region II

B: Antibody 053054 single chain variable fragment

C: Duffy binding surface protein region II

D: Antibody 053054 single chain variable fragment

hetero molecules

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

1

A: Duffy binding surface protein region II

B: Antibody 053054 single chain variable fragment

hetero molecules

defined by author&software
Evidence: gel filtration
65.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Duffy binding surface protein region II

D: Antibody 053054 single chain variable fragment

hetero molecules

defined by author&software
Evidence: gel filtration
65.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.480, 53.950, 142.780
Angle α, β, γ (deg.)	90.00, 113.74, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Duffy binding surface protein region II Mass: 37451.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Production host: Escherichia coli (E. coli) / References: UniProt: B7T089, UniProt: P22290*PLUS
#2: Antibody	Antibody 053054 single chain variable fragment Mass: 27911.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.29 %
Crystal grow	Temperature: 290 K / Method: evaporation / pH: 5.6 Details: 0.2M ammonium sulfate, 0.1 M sodium citrate pH 5.6, 25% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9763 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. obs: 28614 / % possible obs: 98.8 % / Redundancy: 3.7 % / R_merge(I) obs: 0.079 / Net I/σ(I): 14.46
Reflection shell	Resolution: 2.9→3 Å / R_merge(I) obs: 0.72 / Num. unique obs: 2705

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NUV

4nuv

Resolution: 2.9→19.596 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.27

	R_factor	Num. reflection	% reflection
R_free	0.2516	1394	4.88 %
R_work	0.2297	-	-
obs	0.2308	28572	99.19 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.9→19.596 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7717	0	10	6	7733

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7913
X-RAY DIFFRACTION	f_angle_d	0.542	10730
X-RAY DIFFRACTION	f_dihedral_angle_d	16.509	4713
X-RAY DIFFRACTION	f_chiral_restr	0.042	1147
X-RAY DIFFRACTION	f_plane_restr	0.003	1360

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 (%)
2.9-3.0033	0.3877	139	0.3688	2734	X-RAY DIFFRACTION	100
3.0033-3.1231	0.3263	143	0.2986	2663	X-RAY DIFFRACTION	100
3.1231-3.2646	0.31	149	0.2822	2704	X-RAY DIFFRACTION	100
3.2646-3.4359	0.3048	134	0.2856	2677	X-RAY DIFFRACTION	99
3.4359-3.6499	0.2782	144	0.248	2689	X-RAY DIFFRACTION	99
3.6499-3.9296	0.2849	111	0.2371	2667	X-RAY DIFFRACTION	97
3.9296-4.3212	0.2246	141	0.2106	2708	X-RAY DIFFRACTION	100
4.3212-4.9377	0.2079	146	0.1918	2739	X-RAY DIFFRACTION	100
4.9377-6.1883	0.23	145	0.2094	2751	X-RAY DIFFRACTION	100
6.1883-19.5964	0.2283	142	0.2079	2846	X-RAY DIFFRACTION	100

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	4.2499	-2.4854	1.5063	4.9524	-1.3203	4.8387	0.0968	-0.3132	-0.0741	-0.1131	-0.1021	-0.9485	0.2132	0.9511	0.0732	0.5125	0.0383	0.0495	0.8355	0.0827	0.5875	137.3482	-1.9883	74.992
2	5.5904	-0.0933	0.6076	5.8563	-1.034	4.3547	-0.0683	-0.7269	0.1149	0.4784	0.1533	-0.2123	0.0579	0.3881	-0.0844	0.5053	0.0826	-0.0513	0.82	0.1106	0.4759	129.5294	-2.4761	77.6861
3	1.2381	-0.698	-2.772	0.3729	1.3806	6.2859	-0.3698	0.5333	-0.789	-0.6091	0.1946	0.7869	-0.1072	-1.669	-0.2273	1.3681	0.0509	-0.338	1.2117	-0.0288	1.6813	122.2481	-15.08	63.068
4	3.1503	-0.124	0.5938	5.3661	-0.8551	4.0987	0.384	0.6203	-0.5502	-0.7789	0.0599	0.6308	1.0786	-0.5561	-0.3738	0.9949	0.0568	-0.2343	0.9086	0.0124	0.5906	138.3633	-20.172	81.7848
5	1.7427	0.3844	0.8773	4.9183	1.0466	5.6079	0.8719	-0.6628	0.1166	-0.6931	0.2296	-0.7382	0.3295	1.4657	-0.4378	1.0233	0.3267	-0.3093	1.1548	0.0375	0.7442	146.7282	-19.5811	90.3478
6	2.71	0.6763	-2.6956	3.3464	2.9738	6.9847	0.1775	-0.5215	-1.2174	-0.3122	0.1736	0.8561	1.2833	-0.7894	-0.1458	1.2845	-0.0063	-0.2816	0.9882	0.2074	0.9006	137.3888	-26.8218	90.7332
7	3.6951	-2.1806	-0.1424	6.2017	0.3139	6.201	0.0442	0.0956	0.5383	-0.2289	-0.1275	0.6314	-0.6459	-0.8719	0.0912	0.4228	0.0861	-0.0055	0.5434	-0.0286	0.5915	113.2491	17.7099	58.454
8	6.1865	-1.5841	-0.1877	4.0332	-1.1028	4.2529	0.1678	0.3663	-0.5485	-0.8274	-0.0899	-0.5444	0.4532	0.5661	0.1586	0.7442	-0.0246	0.0811	0.6702	0.0592	0.4335	125.5237	5.9153	43.5004
9	5.1172	-0.5789	0.4847	4.134	0.2112	6.1939	-0.0336	0.5084	-0.1578	-0.7123	-0.0484	0.3177	0.2853	-0.4385	-0.0039	0.5536	-0.0191	0.0089	0.4282	0.0356	0.4356	120.0882	1.6053	46.4716
10	4.8923	0.4148	-0.7235	1.8376	0.1908	7.2826	0.1868	0.2897	-0.0918	0.4245	0.5128	-0.3637	1.5272	-1.7624	-0.4011	0.8971	-0.082	-0.0297	1.8514	0.0819	1.1192	136.1623	-17.0943	131.5133
11	4.8694	1.15	1.3323	3.707	0.5213	5.6194	-0.2362	0.504	0.5925	-0.0815	-0.0519	0.4735	-0.4824	-0.5865	0.3371	0.5869	0.1464	-0.041	0.9219	0.0996	0.553	147.1743	-7.492	126.1972
12	2.8426	1.3163	0.5933	3.1668	-0.611	2.7561	-0.2607	0.1129	-0.2795	-0.3097	0.0633	-0.217	0.6321	0.3535	0.0927	0.9766	0.0825	-0.0513	1.0028	0.0758	0.717	145.7321	-22.0007	119.6011
13	1.3518	-1.8228	0.9258	3.8927	0.6077	4.2069	0.1447	0.4747	-0.6514	0.7301	0.3456	0.5335	0.3495	-1.4883	-0.1192	1.0365	-0.054	-0.2226	1.4102	0.1625	1.0287	129.8933	-18.8248	109.9404
14	3.1866	-2.7353	-1.4996	7.5806	-1.1305	1.7647	-0.0729	-0.2915	-0.7267	0.8131	0.082	-1.4128	0.1885	1.3132	0.2929	0.8376	0.1188	-0.2691	1.2591	0.1172	0.8468	146.409	-18.5249	104.7804
15	3.1087	3.0232	-1.6925	4.8818	-0.9347	1.1303	0.1644	0.1778	-0.3574	-1.0787	0.3307	-0.5465	0.2937	-0.488	-0.2133	1.3201	-0.1078	-0.3062	1.3485	0.0556	0.7351	132.4348	-28.3947	104.0842
16	6.6185	1.4566	1.7853	3.0141	2.4595	3.7671	-0.5407	0.5633	0.7336	-0.1815	0.5122	-0.1285	-0.6602	1.2355	0.0769	0.9167	-0.13	0	0.8042	0.148	0.8517	177.4733	5.2278	146.0371
17	4.1005	1.5232	3.0522	5.6896	0.2584	4.9678	-0.4699	0.4638	0.9469	0.175	0.0696	-0.0058	-1.3078	0.171	0.4082	0.794	0.0108	-0.0702	0.5068	0.1826	0.7322	168.9031	5.1166	147.8654
18	4.3214	2.1422	1.9652	3.6953	1.3828	4.4029	-0.2468	0.099	0.4241	0.2328	0.0784	0.0987	-0.3802	-0.2867	0.2507	0.5862	0.1898	-0.0253	0.4452	0.0907	0.5051	166.4381	-5.2521	150.1419
19	6.7936	2.4771	1.0237	3.5778	0.663	5.549	-0.1207	-0.0996	-0.4007	0.6202	0.0067	0.019	0.7905	0.0322	0.0492	0.7182	0.1626	0.131	0.3601	0.0056	0.4371	164.2108	-17.0779	153.9385
20	5.517	0.995	1.402	3.4685	0.8196	7.7118	0.0801	0.3222	-0.4853	0.1538	-0.0643	-0.1557	0.6043	0.3735	-0.0557	0.708	0.0974	0.1219	0.4809	0.0397	0.4992	164.467	-17.1732	151.3417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 216 through 290 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 291 through 368 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 369 through 378 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 379 through 432 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 433 through 462 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 463 through 501 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 119 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 120 through 174 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 175 through 255 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 216 through 225 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 226 through 368 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 369 through 432 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 433 through 462 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 463 through 481 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 482 through 501 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 6 through 37 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 38 through 105 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 106 through 153 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 154 through 192 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 193 through 253 )

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