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- PDB-6o29: Crystal structure of 4493 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6o29
TitleCrystal structure of 4493 Fab in complex with circumsporozoite protein NPDP and anti-kappa VHH domain
Components
  • 4493 Fab heavy chain
  • 4493 Kappa light chain
  • Anti-kappa VHH domain
  • Circumsporozoite protein
KeywordsIMMUNE 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
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
CitationJournal: 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
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: 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 1.2Apr 3, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
H: 4493 Fab heavy chain
L: 4493 Kappa light chain
C: Circumsporozoite protein
D: Circumsporozoite protein
K: Anti-kappa VHH domain
E: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,66511
Polymers120,4798
Non-polymers1863
Water2,144119
1
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
C: Circumsporozoite protein
K: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4267
Polymers60,2404
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 4493 Fab heavy chain
L: 4493 Kappa light chain
D: Circumsporozoite protein
E: Anti-kappa VHH domain


Theoretical massNumber of molelcules
Total (without water)60,2404
Polymers60,2404
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.537, 79.761, 281.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 214)
21(chain H and (resid 1 through 127 or resid 134...
12(chain B and resid 1 through 213)
22(chain L and (resid 1 through 23 or (resid 24...
13(chain C and resid 2 through 15)
23(chain D and resid 2 through 15)
14chain E
24(chain K and resid 1 through 113)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYS(chain A and resid 1 through 214)AA1 - 2141 - 223
211GLUGLUSERSER(chain H and (resid 1 through 127 or resid 134...HC1 - 1271 - 136
221GLYGLYPROPRO(chain H and (resid 1 through 127 or resid 134...HC134 - 213143 - 222
231LYSLYSLYSLYS(chain H and (resid 1 through 127 or resid 134...HC214223
241GLUGLULYSLYS(chain H and (resid 1 through 127 or resid 134...HC1 - 2141 - 223
251GLUGLULYSLYS(chain H and (resid 1 through 127 or resid 134...HC1 - 2141 - 223
261GLUGLULYSLYS(chain H and (resid 1 through 127 or resid 134...HC1 - 2141 - 223
271GLUGLULYSLYS(chain H and (resid 1 through 127 or resid 134...HC1 - 2141 - 223
112GLUGLUGLUGLU(chain B and resid 1 through 213)BB1 - 2131 - 214
212GLUGLUCYSCYS(chain L and (resid 1 through 23 or (resid 24...LD1 - 231 - 23
222ARGARGALAALA(chain L and (resid 1 through 23 or (resid 24...LD24 - 2524 - 25
232GLUGLUGLUGLU(chain L and (resid 1 through 23 or (resid 24...LD1 - 2131 - 214
242GLUGLUGLUGLU(chain L and (resid 1 through 23 or (resid 24...LD1 - 2131 - 214
252GLUGLUGLUGLU(chain L and (resid 1 through 23 or (resid 24...LD1 - 2131 - 214
262GLUGLUGLUGLU(chain L and (resid 1 through 23 or (resid 24...LD1 - 2131 - 214
113PROPROASNASN(chain C and resid 2 through 15)CE2 - 152 - 15
213PROPROASNASN(chain D and resid 2 through 15)DF2 - 152 - 15
114UNKUNKSERSERchain EEH1 - 1131 - 121
214UNKUNKSERSER(chain K and resid 1 through 113)KG1 - 1131 - 121

NCS ensembles :
ID
1
2
3
4

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Components

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Circumsporozoite protein / CS


Mass: 1659.668 Da / Num. of mol.: 2 / Fragment: residues 120-135 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

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Antibody , 3 types, 6 molecules AHBLKE

#1: Antibody 4493 Fab heavy chain


Mass: 23792.730 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 4493 Kappa light chain


Mass: 23460.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Anti-kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 122 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG3350, 0.2 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 49310 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2353 / CC1/2: 0.761 / Rpim(I) all: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house model

Resolution: 2.4→29.589 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1549 3.15 %
Rwork0.2011 47617 -
obs0.2024 49166 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.53 Å2 / Biso mean: 60.1224 Å2 / Biso min: 30.3 Å2
Refinement stepCycle: final / Resolution: 2.4→29.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 12 119 8344
Biso mean--62.47 52.32 -
Num. residues----1140
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1974X-RAY DIFFRACTION6.148TORSIONAL
12H1974X-RAY DIFFRACTION6.148TORSIONAL
21B2010X-RAY DIFFRACTION6.148TORSIONAL
22L2010X-RAY DIFFRACTION6.148TORSIONAL
31C128X-RAY DIFFRACTION6.148TORSIONAL
32D128X-RAY DIFFRACTION6.148TORSIONAL
41E1123X-RAY DIFFRACTION6.148TORSIONAL
42K1123X-RAY DIFFRACTION6.148TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.47740.37211400.30814300
2.4774-2.56590.30021380.29774221
2.5659-2.66860.36041380.2914243
2.6686-2.790.37161380.27924251
2.79-2.93690.30991400.26814308
2.9369-3.12080.32441390.24884278
3.1208-3.36140.28091410.24634332
3.3614-3.69910.24871400.20454296
3.6991-4.2330.23271430.17584389
4.233-5.32810.14431430.1374396
5.3281-29.5890.18311490.15534603
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.5705-0.6247-2.16220.15690.14252.6427-0.04490.2966-0.0196-0.23250.04660.16560.2807-0.52570.01830.7331-0.1668-0.08730.75930.07850.47468.22241.498667.1835
23.26960.88820.1893.18422.37534.1265-0.11310.10250.6737-0.2231-0.00840.2516-0.5232-0.05460.1230.39010.0499-0.07880.51270.05530.7199-4.754515.788998.5858
32.26720.26560.13153.52591.19785.3266-0.10270.0703-0.0432-0.42140.2393-0.08250.08340.0754-0.15650.4538-0.06430.00420.53170.0810.44122.9117-4.757582.9209
47.78630.67680.25580.34720.61371.2689-0.0207-0.04850.4198-0.0341-0.06240.10790.0232-0.05710.08040.33040.0495-0.03670.47620.01250.4875-3.0550.9482106.1163
53.88331.4209-1.8081.0156-0.68064.5310.0768-0.3795-0.14720.382-0.1687-0.19620.29770.57650.08870.64850.023-0.060.5311-0.00010.395642.181.642447.9057
64.9421-1.37111.20283.8085-2.3726.17720.00570.13780.3243-0.1453-0.0507-0.5-0.42260.48380.05280.3004-0.11620.01870.436-0.04780.497554.626515.887915.4827
72.19070.1420.91672.4056-1.87778.54010.06910.0248-0.14460.27630.0450.1490.526-0.1725-0.14130.4481-0.00730.03120.3018-0.03160.403827.4913-4.670132.1763
85.038-0.4602-0.52130.88340.36881.65190.09690.43750.1237-0.1064-0.0966-0.11380.04030.33050.00210.36250.0087-0.0010.48930.02910.42153.54611.39199.0796
98.9853-4.2936-5.47297.5245.21194.5689-0.16880.1411-1.3290.061-0.37831.01990.26031.03010.71051.0947-0.1882-0.11810.83570.09090.601718.4431-13.477558.7092
105.0052-0.60180.23948.89842.14457.84020.3058-1.4734-1.27650.5383-0.0856-0.87930.0588-0.6185-0.11651.0418-0.0815-0.14430.83970.19570.670932.208-12.898857.4987
112.5710.0929-0.02442.67340.04543.2756-0.0981-0.19710.16860.20160.0644-0.1053-0.02530.15250.02580.32630.07370.00030.48920.02440.428420.9432-11.6077115.9352
123.6524-1.13771.21763.08970.24276.17980.15730.4668-0.3171-0.0801-0.05450.12030.32390.2686-0.06680.33830.02120.01270.3606-0.07420.471929.9831-12.1115-0.6341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 214 )A114 - 214
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 213 )B108 - 213
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 113 )H1 - 113
6X-RAY DIFFRACTION6chain 'H' and (resid 114 through 214 )H114 - 214
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 107 )L1 - 107
8X-RAY DIFFRACTION8chain 'L' and (resid 108 through 213 )L108 - 213
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 15 )C1 - 15
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 16 )D2 - 16
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 113 )K1 - 113
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 113 )E1 - 113

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