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- PDB-2ypv: Crystal structure of the Meningococcal vaccine antigen factor H b... -

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Basic information

Entry
Database: PDB / ID: 2ypv
TitleCrystal structure of the Meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody
Components
  • (FAB 12C1) x 2
  • LIPOPROTEIN
KeywordsIMMUNE SYSTEM / VACCINE / MONOCLONAL ANTIBODY / MAB / EPITOPE MAPPING
Function / homology
Function and homology information


bacterial extracellular vesicle / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #1980 / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Immunoglobulin-like - #1980 / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Factor H-binding protein / Factor H binding protein
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS MC58 (bacteria)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMalito, E. / Veggi, D. / Bottomley, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Defining a Protective Epitope on Factor H Binding Protein, a Key Meningococcal Virulence Factor and Vaccine Antigen.
Authors: Malito, E. / Faleri, A. / Lo Surdo, P. / Veggi, D. / Maruggi, G. / Grassi, E. / Cartocci, E. / Bertoldi, I. / Genovese, A. / Santini, L. / Romagnoli, G. / Borgogni, E. / Brier, S. / Lo ...Authors: Malito, E. / Faleri, A. / Lo Surdo, P. / Veggi, D. / Maruggi, G. / Grassi, E. / Cartocci, E. / Bertoldi, I. / Genovese, A. / Santini, L. / Romagnoli, G. / Borgogni, E. / Brier, S. / Lo Passo, C. / Domina, M. / Castellino, F. / Felici, F. / Van Der Veen, S. / Johnson, S. / Lea, S.M. / Tang, C.M. / Pizza, M. / Savino, S. / Norais, N. / Rappuoli, R. / Bottomley, M.J. / Masignani, V.
History
DepositionNov 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOPROTEIN
H: FAB 12C1
L: FAB 12C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63712
Polymers74,0783
Non-polymers5599
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-38.4 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.800, 81.850, 152.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LIPOPROTEIN / LIPOPROTEIN GNA1870 / FACTOR H BINDING PROTEIN


Mass: 26838.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Variant: 1.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QCC2, UniProt: Q9JXV4*PLUS
#2: Antibody FAB 12C1


Mass: 23395.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody FAB 12C1


Mass: 23844.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE MAB 12C1 WAS FULLY SEQUENCED ISOLATING RNA FROM MURINE HYBRIDOMA CELLS, FROM WHICH CDNA WAS ...THE MAB 12C1 WAS FULLY SEQUENCED ISOLATING RNA FROM MURINE HYBRIDOMA CELLS, FROM WHICH CDNA WAS PREPARED USING STANDARD METHODS. THE MAB HEAVY AND LIGHT CHAINS WERE AMPLIFIED FROM THE CDNA BY PCR USING A SET OF DEGENERATE PRIMERS DESIGNED BASED ON MOUSE FRAMEWORKS SEQUENCES.

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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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: NONE
Crystal growpH: 8.5 / Details: 20% PEG 3350, 0.2M AMMONIUM SULFATE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.53 Å / Num. obs: 69157 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 22.54 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.62
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2W80 1KB5 3LIZ

2w80

1kb5

3liz


Resolution: 1.8→39.531 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 22.11 / Stereochemistry target values: ML
Details: DISORDERED REGIONS IN CHAIN A INCLUDE RESIDUES V8-A14 E83- Q87 AND Q115-K122. DISORDERED REGION IN CHAIN H INCLUDE RESIDUES G135-T137.
RfactorNum. reflection% reflection
Rfree0.2246 3503 5.1 %
Rwork0.1812 --
obs0.1834 69144 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 36 464 5518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135169
X-RAY DIFFRACTIONf_angle_d1.5146978
X-RAY DIFFRACTIONf_dihedral_angle_d13.9551872
X-RAY DIFFRACTIONf_chiral_restr0.111776
X-RAY DIFFRACTIONf_plane_restr0.006894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.32411470.27062594X-RAY DIFFRACTION100
1.8247-1.85070.32481550.25282585X-RAY DIFFRACTION100
1.8507-1.87830.29551210.23142567X-RAY DIFFRACTION100
1.8783-1.90770.27521210.21992659X-RAY DIFFRACTION100
1.9077-1.9390.28251380.22112551X-RAY DIFFRACTION100
1.939-1.97240.261460.2062614X-RAY DIFFRACTION100
1.9724-2.00830.24391330.20472598X-RAY DIFFRACTION100
2.0083-2.04690.23571350.19632610X-RAY DIFFRACTION100
2.0469-2.08870.2611640.19682547X-RAY DIFFRACTION100
2.0887-2.13410.24371320.18832596X-RAY DIFFRACTION100
2.1341-2.18370.24671630.18962610X-RAY DIFFRACTION100
2.1837-2.23830.24131290.1792598X-RAY DIFFRACTION100
2.2383-2.29880.23291500.18232585X-RAY DIFFRACTION100
2.2988-2.36650.22081460.17472594X-RAY DIFFRACTION100
2.3665-2.44290.19751350.18092634X-RAY DIFFRACTION100
2.4429-2.53020.23131320.1782611X-RAY DIFFRACTION100
2.5302-2.63140.22631430.18222627X-RAY DIFFRACTION100
2.6314-2.75120.24771280.19242638X-RAY DIFFRACTION100
2.7512-2.89620.2261440.18412623X-RAY DIFFRACTION100
2.8962-3.07760.24841520.18692626X-RAY DIFFRACTION100
3.0776-3.31510.25611410.19012645X-RAY DIFFRACTION100
3.3151-3.64850.18751300.17112678X-RAY DIFFRACTION100
3.6485-4.17590.20181360.15832684X-RAY DIFFRACTION100
4.1759-5.25930.15661310.13782735X-RAY DIFFRACTION100
5.2593-39.54030.21381510.192832X-RAY DIFFRACTION100

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