PDB-6ule: Crystal structure of 2541 Fab in complex with circumsporozoite pr...

ID or keywords:

Entry

Database: PDB / ID: 6ule

Title

Crystal structure of 2541 Fab in complex with circumsporozoite protein NANP5

Components

2541 Antibody, heavy chain
2541 Antibody, light chain
Circumsporozoite protein

Keywords

IMMUNE SYSTEM / Malaria / Antibody

Function / homology

Function and homology information

entry into host cell by a symbiont-containing vacuole / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Thai, E. / Scally, S.W. / Murugan, R. / Wardemann, H. / Julien, J.P.

Funding support

United States, 1items

Citation

Journal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.

History

Deposition	Oct 7, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 10, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: 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	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 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ule.cif.gz	425.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ule_validation.pdf.gz	455.2 KB	Display	wwPDB validaton report
Full document	6ule_full_validation.pdf.gz	464.5 KB	Display
Data in XML	6ule_validation.xml.gz	32.1 KB	Display
Data in CIF	6ule_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/6ule ftp://data.pdbj.org/pub/pdb/validation_reports/ul/6ule	HTTPS FTP

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Related structure data

Related structure data	6o23C 6o24C 6o25C 6o26C 6o28C 6o29C 6o2aC 6o2bC 6o2cC 6ulfC 6vlnC 6d01S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6o23-d 2or9-d 1bln-d 5dyo-d 6dg2-d 6axl-d 6q27-d 6d01-1 3q6i-d 5izk-d 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)

Deposited unit

A: 2541 Antibody, heavy chain

B: 2541 Antibody, light chain

C: 2541 Antibody, heavy chain

D: 2541 Antibody, light chain

I: Circumsporozoite protein

97.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	66.770, 63.694, 146.654
Angle α, β, γ (deg.)	90.000, 100.997, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Antibody	2541 Antibody, heavy chain Mass: 24263.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	2541 Antibody, light chain Mass: 23444.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide	Circumsporozoite protein / CS Mass: 2000.006 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.17 Å³/Da / Density % sol: 61.25 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulfate, 0.1 M citric acid pH 3.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033167 Å / Relative weight: 1
Reflection	Resolution: 2.55→40 Å / Num. obs: 39583 / % possible obs: 99.4 % / Redundancy: 6.8 % / B_iso Wilson estimate: 69.82 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.039 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.55→2.59 Å / R_merge(I) obs: 0.749 / Num. unique obs: 1755 / CC_1/2: 0.701

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6D01

6d01

Resolution: 2.55→38.33 Å / SU ML: 0.4834 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.6839

	R_factor	Num. reflection	% reflection
R_free	0.2588	1976	5 %
R_work	0.2085	-	-
obs	0.211	39506	99.28 %

Solvent computation

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

Displacement parameters

B_iso mean: 86.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→38.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6746	0	0	93	6839

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6955
X-RAY DIFFRACTION	f_angle_d	0.5057	9486
X-RAY DIFFRACTION	f_chiral_restr	0.0411	1065
X-RAY DIFFRACTION	f_plane_restr	0.0038	1212
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3085	4160

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 (%)
2.55-2.61	0.4117	133	0.3581	2621	X-RAY DIFFRACTION	98.39
2.61-2.68	0.4041	136	0.3484	2640	X-RAY DIFFRACTION	98.75
2.68-2.76	0.3176	144	0.3268	2648	X-RAY DIFFRACTION	98.62
2.76-2.85	0.3849	143	0.3087	2642	X-RAY DIFFRACTION	99.04
2.85-2.95	0.3965	135	0.3243	2654	X-RAY DIFFRACTION	98.94
2.95-3.07	0.4006	147	0.3123	2685	X-RAY DIFFRACTION	99.09
3.07-3.21	0.4052	142	0.291	2665	X-RAY DIFFRACTION	99.5
3.21-3.38	0.2847	143	0.2473	2677	X-RAY DIFFRACTION	99.58
3.38-3.59	0.2796	138	0.2134	2676	X-RAY DIFFRACTION	99.58
3.59-3.87	0.2317	139	0.2007	2683	X-RAY DIFFRACTION	99.61
3.87-4.26	0.2168	140	0.1613	2703	X-RAY DIFFRACTION	99.48
4.26-4.88	0.1877	145	0.1404	2714	X-RAY DIFFRACTION	99.86
4.88-6.14	0.2138	144	0.173	2734	X-RAY DIFFRACTION	99.76
6.14-38.33	0.2373	147	0.1979	2788	X-RAY DIFFRACTION	99.63

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	1.77375020478	0.331660086558	-0.0881940383769	5.07208856601	-4.20000236465	5.52414324404	0.30700784703	-0.609429480171	-0.142184910781	0.683466697029	-0.674308602349	-0.691563744424	-0.534652676805	0.760056974988	0.33248474501	0.815117466435	-0.186175962895	-0.021375095335	0.655437533376	0.106244917602	0.561945925736	9.99941420054	18.4589172246	31.0292178048
2	8.74154557916	-2.46711941266	1.16123242836	4.17411933565	-0.737151594968	2.42606097807	-0.29026236026	-0.116542645858	0.301223196853	0.107990716079	0.0156168176435	-0.0502224571959	-0.380866757491	-0.0892006960157	0.241654895264	0.915557897974	9.25611614305E-5	0.178501057442	0.380857233451	0.0338324860747	0.474896009925	-4.2031204027	42.2231358988	8.14879670099
3	6.14526662156	-2.02065062295	1.08794321707	4.50281245542	-0.991230886988	3.10103333197	0.307488644571	-0.47841307275	-0.283522165174	0.302354870507	0.0246110734234	0.288680397065	0.143010027494	-0.718698231306	-0.317663935428	0.768881945558	-0.0832223223644	0.0907669698169	0.652941859475	0.112790677923	0.457310278207	-11.1422831863	12.4649389927	30.2946213435
4	5.91885066581	-0.111775731206	-1.27271520314	1.63068330134	-0.0652162913212	5.0552852929	0.15360669388	-0.0629178651281	-0.0175869335891	-0.329599442917	0.00812282474276	0.0408295128603	-0.346623151048	-0.11830854317	-0.15863377248	0.913899405835	0.0316358772957	0.162154989356	0.352822549726	0.0822104666766	0.554463394137	-10.0728669916	29.6883672455	0.709652309014
5	1.78193782555	1.08236262966	0.854103982192	3.15622385805	1.90622033397	4.21222326954	0.0671690416359	-0.0947373366629	-0.0592730421729	-0.000643139391314	-0.0858653207993	-0.180906231091	-0.125696199588	0.0122480736485	-0.00127674140356	0.540808960945	-0.0414902949454	0.102069589515	0.521995403337	0.116043855959	0.523971168586	12.3832040991	2.01949103093	71.1307204319
6	3.99494193828	2.98362397687	-4.63293793867	4.32633698444	-3.77362034648	5.09041030641	0.0492497719423	-0.22270060554	0.174738515833	0.647997397718	0.100545163021	0.316519682038	-0.333700135389	-0.117510449917	-0.095720916584	0.923215145888	-0.194229346942	0.212983219072	1.12451240632	-0.121362615032	0.634819759632	1.37138016505	5.95223323546	104.980390704
7	7.04445517701	0.249510528956	-0.594631059817	4.14834455526	1.47477996012	8.39647602004	0.094051702133	-0.596880627747	0.113278018451	0.106403031688	-0.29303147007	0.952585033047	-0.0174354553505	-1.99079502522	0.16910878645	0.463119060094	-0.010782223206	0.0116665809227	0.925993849476	0.0171321530309	0.657686184506	-9.34116970419	-0.219081300898	68.8920645115
8	2.20833771937	1.23396434121	0.910786664364	3.24877225546	0.703494517478	1.08517161468	-0.0320352190033	-0.138458831954	0.269002265543	0.373697987519	-0.368360101533	0.595034765189	0.0999557664364	-1.04393916001	0.359138175219	0.984859453508	-0.0487961058487	0.257967348752	1.46021927876	-0.150405606678	0.780983780499	-8.93844666997	16.9777832771	99.4822959536
9	2.86113160034	0.986149001389	0.640695989329	1.22618160726	-2.09359495999	7.99834034538	-0.334070474821	0.322663117629	0.145800781368	-1.18163963003	0.488501126089	0.23988010476	-0.379451687836	0.131524262341	-0.16028449451	0.867261447968	-0.117372838888	0.028302168776	0.697535862841	0.0770771163555	0.563260915769	7.39039621727	0.835746117019	47.5483785159

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 through 123	A	0
2	X-RAY DIFFRACTION	2	chain 'A' and resid 124 through 225	A	0
3	X-RAY DIFFRACTION	3	chain 'B' and resid 1 through 106	B	0
4	X-RAY DIFFRACTION	4	chain 'B' and resid 107 through 213	B	0
5	X-RAY DIFFRACTION	5	chain 'C' and resid 1 through 123	C	0
6	X-RAY DIFFRACTION	6	chain 'C' and resid 124 through 224	C	0
7	X-RAY DIFFRACTION	7	chain 'D' and resid 1 through 106	D	0
8	X-RAY DIFFRACTION	8	chain 'D' and resid 107 through 213	D	0
9	X-RAY DIFFRACTION	9	chain 'I'	I	3 - 19

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