PDB-6vln: Crystal structure of 4498 Fab in complex with circumsporozoite pr...

ID or keywords:

Entry

Database: PDB / ID: 6vln

Title

Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and anti-Kappa VHH domain

Components

4498 Fab heavy chain
4498 Fab light chain
Circumsporozoite protein
anti Kappa VHH domain

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)

Camelidae mixed library (mammal)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Thai, E. / Scally, S.W. / Prieto, K. / 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	Jan 24, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 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 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vln.cif.gz	283.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6vln.ent.gz	188.6 KB	Display	PDB format
PDBx/mmJSON format	6vln.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vln_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	6vln_full_validation.pdf.gz	464.4 KB	Display
Data in XML	6vln_validation.xml.gz	26.3 KB	Display
Data in CIF	6vln_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/6vln ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vln	HTTPS FTP

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Related structure data

Related structure data	6o23C 6o24C 6o25C 6o26C 6o28C 6o29C 6o2aC 6o2bC 6o2cC 6uleC 6ulfC 6d01S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ulf-d 6fpy-2 4iw3-2 4pkr-d 1xf5-1 2vl7-d 4yk0-d 5ze3-1 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

H: 4498 Fab heavy chain

L: 4498 Fab light chain

K: anti Kappa VHH domain

P: Circumsporozoite protein

hetero molecules

60.8 kDa, 4 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)	62.204, 76.481, 63.693
Angle α, β, γ (deg.)	90.000, 98.761, 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

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Protein/peptide , 1 types, 1 molecules P

#4: Protein/peptide	Circumsporozoite protein / CS Mass: 1265.286 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893

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Antibody , 3 types, 3 molecules HLK

#1: Antibody	4498 Fab heavy chain Mass: 24749.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	4498 Fab light chain Mass: 23371.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	anti Kappa VHH domain Mass: 11326.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Camelidae mixed library (mammal)

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Non-polymers , 2 types, 486 molecules

#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.58 Å³/Da / Density % sol: 52.35 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M phosphate-citrate pH 4.2, 20% (w/v) polyethylene glycol 8000, 0.2 M sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03319 Å / Relative weight: 1
Reflection	Resolution: 1.63→40 Å / Num. obs: 73553 / % possible obs: 99.9 % / Redundancy: 6.7 % / B_iso Wilson estimate: 23.37 Å² / CC_1/2: 0.99 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.63→1.65 Å / Num. unique obs: 2626 / CC_1/2: 0.83

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6D01

6d01

Resolution: 1.63→38.24 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2343	1984	2.7 %
R_work	0.2094	71502	-
obs	0.2101	73486	99.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.63→38.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4158	0	6	485	4649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0125	4333
X-RAY DIFFRACTION	f_angle_d	1.2343	5939
X-RAY DIFFRACTION	f_chiral_restr	0.0803	682
X-RAY DIFFRACTION	f_plane_restr	0.0086	771
X-RAY DIFFRACTION	f_dihedral_angle_d	18.5409	1492

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 (%)
1.63-1.67	0.3656	143	0.3187	5073	X-RAY DIFFRACTION	99.89
1.67-1.72	0.3035	134	0.2812	5087	X-RAY DIFFRACTION	99.83
1.72-1.77	0.318	141	0.2608	5070	X-RAY DIFFRACTION	99.88
1.77-1.82	0.2593	146	0.2438	5112	X-RAY DIFFRACTION	99.85
1.82-1.89	0.2716	142	0.2259	5065	X-RAY DIFFRACTION	99.87
1.89-1.96	0.2442	140	0.2197	5088	X-RAY DIFFRACTION	99.85
1.96-2.05	0.2805	140	0.2047	5105	X-RAY DIFFRACTION	99.94
2.05-2.16	0.2211	136	0.2092	5093	X-RAY DIFFRACTION	99.89
2.16-2.3	0.2573	147	0.2082	5101	X-RAY DIFFRACTION	99.92
2.3-2.47	0.2446	143	0.2155	5126	X-RAY DIFFRACTION	99.96
2.47-2.72	0.2753	142	0.2217	5092	X-RAY DIFFRACTION	99.98
2.72-3.12	0.2413	140	0.2071	5136	X-RAY DIFFRACTION	99.92
3.12-3.93	0.2235	147	0.1906	5128	X-RAY DIFFRACTION	99.94
3.93-38.24	0.1837	143	0.1963	5226	X-RAY DIFFRACTION	99.87

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	2.78431051229	1.60431063571	1.41366433323	5.28408540024	0.69262336966	8.74358699311	0.151275211961	-0.321487081618	-0.417222562549	0.646083656646	0.0495884752148	-0.465499850342	0.248179508229	0.614302488727	-0.238485886168	0.271790283109	0.0244479107583	-0.0525082895531	0.295668209984	0.0247353702525	0.223021478389	10.0341518166	-16.104520107	25.2864261792
2	4.05146730959	3.48853234189	-2.39743456508	2.00739444197	-1.16940857975	8.21951485737	0.4540412638	0.111067606183	-0.557816154052	-0.0494794679559	-0.326607084586	-1.53792616301	0.657518439022	0.859359424647	-0.274131318213	0.347266707581	0.205467230921	-0.0943713345565	0.643778583837	0.139225377833	0.728494645603	38.6177619588	-5.69088924799	18.9349057373
3	2.44444355349	-1.29177443377	0.364208196181	4.88270306304	0.568990699783	3.32854077174	-0.0168070154685	-0.132189203677	-0.00425888198575	0.453575946939	0.0463898315931	-0.369050366611	0.00848761678088	0.380046766538	-0.0135747018182	0.28819240937	0.0106266623155	-0.0710774834995	0.257080962293	0.0346749850466	0.239570547011	26.1659178872	0.997443209636	28.2514432999
4	3.26161795997	1.98542475648	0.490865877716	3.22374952205	-1.90824549997	2.58228651197	-0.0902080603986	0.544931600877	-0.877406802128	-0.00153040154358	-0.19010774974	-0.665638557333	0.976765120334	0.796763315827	0.213474400503	0.400022773358	0.198510826652	-0.0657020514358	0.449155552342	-0.0201575453186	0.458685443944	29.2333053633	-6.99958254248	15.0623361726
5	1.73538557828	-0.686675735128	-0.40994147511	0.830353087421	0.689666696705	0.596306415545	0.0269654544961	0.097237735166	0.0523891576897	-0.0722657031965	-0.0418492437594	-0.0182695974227	0.125503911708	-0.0341340567486	0.0307132055495	0.305106343901	-0.0371675219895	0.0152859830942	0.207790283486	0.0360184559993	0.168380426377	0.574423627672	15.7886269939	23.2542118442
6	6.69354712934	-0.611770410024	2.69607159493	1.5978987983	-0.0426731731728	5.89593116937	-0.0645869896576	-0.125599431016	-0.00328676878741	0.000139734947457	0.0806310119576	0.247697728221	-0.026267370973	-0.569748600015	0.00817922005627	0.287458719843	-0.0460215746226	0.0248580490776	0.159935952828	-0.010145093983	0.168694655413	-11.1155253444	18.5503327602	23.9240610824
7	5.83623445542	-0.0131115785645	-1.12247254772	3.73353392492	-0.447849718138	0.268783528731	0.27475676474	-0.190291410569	0.227652441886	-0.22642357544	-0.381783382591	-0.454188084292	-0.232997941364	0.291912509507	0.219423947118	0.348079753153	-0.0263262842289	0.0515935885736	0.258190104864	0.0989860980358	0.233095421994	18.9684487441	8.21430497489	0.78737419261
8	4.20398018335	-0.285566647788	2.4661041164	2.26431421827	0.858895973501	3.42657997297	0.0725263042876	0.438999265869	-0.0400502406091	-0.17624618359	-0.067967780963	-0.367275857313	0.106821439303	0.709086960511	0.0210611640505	0.248804167804	0.0583496297058	0.0391853819274	0.315888063136	0.0598596591249	0.221975422437	22.2528346662	-0.0943969373684	4.27031295168
9	6.73182718741	-3.76079477197	3.95023701179	3.16909303271	-2.40017503129	3.16610847716	0.0031002526539	0.294074045827	0.160690289716	0.00485766066194	-0.246988402697	-0.43292947548	-0.00541280891642	0.4971156731	0.226138980501	0.225527792375	-0.0252145166461	0.0342353961471	0.279574529957	0.0642189941132	0.250124353417	17.5719186304	8.92222755432	6.52098941292
10	1.08483190284	-0.893139040161	-0.0568767045109	3.32196949126	1.38677513211	2.06559110259	-0.0595663741493	-0.103851442604	0.12894435758	0.283883367962	0.106726040381	-0.0991975946588	-0.172165881359	0.149891143188	-0.0329746703246	0.272545184072	-0.0484052848692	-0.00304248768457	0.161247403524	0.010851938145	0.137045013492	-0.20947221773	28.3951687016	14.3899832671
11	0.893094361148	-1.21928825908	-0.488609466769	4.32049376154	2.30328205099	4.3593006211	-0.0283474009763	-0.018866164331	0.0206568356464	0.212237302596	-0.00725900895852	0.0853999557599	-0.289746046169	0.0584982979787	-0.00269341515651	0.226048044272	-0.0600167952748	0.00340300281646	0.159038754287	0.00183378951603	0.141984780846	-2.26423691498	29.7153652479	12.4686250071
12	5.41560951486	-1.93514474544	-1.57484912921	4.38660261634	1.764595683	0.823980638225	0.0232190265591	0.0177573884192	0.21876536381	0.477334148339	-0.075400272193	-0.0833080566813	-0.157284227205	0.0084747028586	0.132822487772	0.300559563569	0.0133120759461	0.0162041669517	0.225300252876	0.0263266510796	0.165428113472	-1.04735256167	-13.3518887044	23.3003046088
13	6.06886514277	2.79228948177	1.12780185866	1.2841296887	0.518718346668	0.21151008912	-0.64260467397	-0.243778606382	0.319815756066	0.238592136192	0.302565495989	0.397123920255	-0.482575658524	0.177111411358	0.385943798189	0.29919684017	0.0675012233841	-0.0189550422196	0.430744675922	0.072571537255	0.256570551217	-14.9944199774	-9.29388673077	12.216397195
14	5.01657443613	-1.32628521489	2.56064370825	1.44549851379	-0.557634745879	3.96182835521	-0.0730278916751	-0.0158056812319	0.214959227749	0.0776716289519	-0.0211130757106	-0.210479267843	-0.271906872424	0.13995430491	0.19952592667	0.225220633705	0.00936419184534	0.000232490931302	0.154954578534	0.020845439253	0.129927632033	0.5055129311	-15.0126247061	11.6476930896
15	2.02890651764	-0.660978227401	6.25924398612	5.00567842797	-1.27652088729	7.38384136104	0.0077504575868	-0.00604514961227	-0.392899107396	-0.189298756765	0.0924950307356	-0.248023515876	0.50239149644	0.354110481909	-0.271971799271	0.237199627913	0.0532097703927	0.00982121560689	0.246548329366	0.00533933399801	0.207130911944	2.4590242143	-24.9751423717	11.6914522074
16	0.865650347731	0.298791242654	0.405607759424	0.908035198391	-0.638410557215	2.9437721964	-0.0224362055114	0.00685819240943	0.0777094580031	0.0452776925178	-0.012442662213	0.0468639827467	-0.176564356744	0.0228731677759	0.0305309459079	0.214503552158	0.0197527478975	0.00384225198153	0.20317811418	0.00349887902944	0.194138478435	-2.70188013048	-14.3681864623	15.3297352675

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'K' and (resid 115 through 121 )
2	X-RAY DIFFRACTION	2	chain 'P' and (resid 2 through 11 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 1 through 87 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 88 through 100I)
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 100J through 175 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 176 through 216 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 18 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 19 through 90 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 91 through 113 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 114 through 163 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 164 through 214 )
12	X-RAY DIFFRACTION	12	chain 'K' and (resid 1 through 25 )
13	X-RAY DIFFRACTION	13	chain 'K' and (resid 26 through 33 )
14	X-RAY DIFFRACTION	14	chain 'K' and (resid 34 through 57 )
15	X-RAY DIFFRACTION	15	chain 'K' and (resid 58 through 67 )
16	X-RAY DIFFRACTION	16	chain 'K' and (resid 68 through 114 )

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Antibody , 3 types, 3 molecules HLK

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Non-polymers , 2 types, 486 molecules

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-Antibody , 3 types, 3 molecules HLK

-Non-polymers , 2 types, 486 molecules

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Related structure data

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Links

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Assembly

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Components

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Protein/peptide , 1 types, 1 molecules P

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Antibody , 3 types, 3 molecules HLK

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Non-polymers , 2 types, 486 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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