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- PDB-6d11: Crystal structure of 1450 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6d11
TitleCrystal structure of 1450 Fab in complex with circumsporozoite protein NANP5
Components
  • 1450 Antibody, Heavy chain
  • 1450 Antibody, Light chain
  • NANP5
KeywordsIMMUNE SYSTEM / Malaria / Antibody / Circumsporozoite protein
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsScally, S.W. / Bosch, A. / Imkeller, K. / Wardemann, H. / Julien, J.P.
CitationJournal: Science / Year: 2018
Title: Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope.
Authors: Imkeller, K. / Scally, S.W. / Bosch, A. / Marti, G.P. / Costa, G. / Triller, G. / Murugan, R. / Renna, V. / Jumaa, H. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Mordmuller, B. / ...Authors: Imkeller, K. / Scally, S.W. / Bosch, A. / Marti, G.P. / Costa, G. / Triller, G. / Murugan, R. / Renna, V. / Jumaa, H. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 4, 2018Group: 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.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1450 Antibody, Heavy chain
B: 1450 Antibody, Light chain
C: 1450 Antibody, Heavy chain
D: 1450 Antibody, Light chain
E: NANP5


Theoretical massNumber of molelcules
Total (without water)96,8295
Polymers96,8295
Non-polymers00
Water00
1
A: 1450 Antibody, Heavy chain
B: 1450 Antibody, Light chain


Theoretical massNumber of molelcules
Total (without water)47,4152
Polymers47,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-20 kcal/mol
Surface area19730 Å2
MethodPISA
2
C: 1450 Antibody, Heavy chain
D: 1450 Antibody, Light chain
E: NANP5


Theoretical massNumber of molelcules
Total (without water)49,4153
Polymers49,4153
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-25 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 135.058, 344.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody 1450 Antibody, Heavy chain


Mass: 23989.707 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 1450 Antibody, Light chain


Mass: 23425.027 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 NANP5


Mass: 2000.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22.5% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 15950 / % possible obs: 92.1 % / Redundancy: 3.9 % / CC1/2: 0.957 / Rmerge(I) obs: 0.311 / Rpim(I) all: 0.165 / Net I/σ(I): 4.5
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2452 / CC1/2: 0.496 / Rpim(I) all: 0.386 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→39.49 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.92
RfactorNum. reflection% reflection
Rfree0.2993 796 5.01 %
Rwork0.2541 --
obs0.2563 15892 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 0 0 6524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026684
X-RAY DIFFRACTIONf_angle_d0.6929118
X-RAY DIFFRACTIONf_dihedral_angle_d13.1453952
X-RAY DIFFRACTIONf_chiral_restr0.0441023
X-RAY DIFFRACTIONf_plane_restr0.0051179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.61310.34291300.29772458X-RAY DIFFRACTION92
3.6131-3.89180.3821320.30462512X-RAY DIFFRACTION95
3.8918-4.2830.2781350.25762542X-RAY DIFFRACTION93
4.283-4.90180.28121290.22382461X-RAY DIFFRACTION93
4.9018-6.17190.31741340.25262528X-RAY DIFFRACTION93
6.1719-39.49230.25681360.23342595X-RAY DIFFRACTION91

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