[English] 日本語
Yorodumi
- PDB-2j5l: Structure of a Plasmodium falciparum apical membrane antigen 1-Fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j5l
TitleStructure of a Plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex
Components
  • (FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19) x 2
  • APICAL MEMBRANE ANTIGEN 1
KeywordsIMMUNE SYSTEM / MALARIA VACCINE CANDIDATE / APICAL MEMBRANE ANTIGEN 1 / HYPOTHETICAL PROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / MEROZOITE / TRANSMEMBRANE / IMMUNOGLOBULIN C REGION / ANTIBODY CROSS-REACTIVITY
Function / homology
Function and homology information


: / membrane => GO:0016020 / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site ...Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Apical membrane antigen 1 / Apical membrane antigen 1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIgonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Cross-Reactivity Studies of an Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding and Structural Characterisation.
Authors: Igonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
History
DepositionSep 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Other / Polymer sequence / Category: entity_poly / pdbx_database_status
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN 1
B: FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
C: FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19


Theoretical massNumber of molelcules
Total (without water)114,5103
Polymers114,5103
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)171.900, 171.900, 44.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein APICAL MEMBRANE ANTIGEN 1 / / PLASMODIUM FALCIPARUM APICAL MEMBRANE ANTIGEN 1


Mass: 67035.547 Da / Num. of mol.: 1 / Fragment: PFAMA1 ECTOPLASMIC REGION, RESIDUES 25-605 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: FVO / Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9GVB7, UniProt: Q9BIM8*PLUS
#2: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19


Mass: 23285.621 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT FAB, LIGHT CHAIN / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C / References: UniProt: Q5XFY8*PLUS
#3: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19


Mass: 24189.033 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT FAB, HEAVY CHAIN / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA. / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 162 TO LYS ENGINEERED RESIDUE IN CHAIN A, THR 288 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ASN 162 TO LYS ENGINEERED RESIDUE IN CHAIN A, THR 288 TO VAL ENGINEERED RESIDUE IN CHAIN A, SER 373 TO ASP ENGINEERED RESIDUE IN CHAIN A, ASN 422 TO SER ENGINEERED RESIDUE IN CHAIN A, SER 423 TO LYS ENGINEERED RESIDUE IN CHAIN A, ASN 499 TO GLN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / pH: 4.6
Details: CRYSTALLISATION TRIALS WERE CARRIED OUT WITH PFAMA1 ECTOPLASMIC CONSTRUCTION CORRESPONDING TO DOMAINS II-III. THE FAB FRAGMENT WAS INCUBATED IN SMALL STOICHIOMETRIC EXCESS WITH THE ...Details: CRYSTALLISATION TRIALS WERE CARRIED OUT WITH PFAMA1 ECTOPLASMIC CONSTRUCTION CORRESPONDING TO DOMAINS II-III. THE FAB FRAGMENT WAS INCUBATED IN SMALL STOICHIOMETRIC EXCESS WITH THE RECOMBINANT PROTEIN (1.2:1) BEFORE ADDING CRYSTALLISATION BUFFERS. CRYSTALLISATION DROPS WERE PREPARED BY MIXING 0.8 MICROL OF PROTEIN WITH 0.8 MICROL OF RESERVOIR BUFFER COMPRISING 12% PEG 6000 AND 0.1 M SODIUM ACETATE AT PH 4.6. THE FINAL PROTEIN CONCENTRATION WAS 3.2 MG/ML. CRYSTALS APPEARED AFTER 5 DAYS AT 17 DEGREE C.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.949
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 18102 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→3 Å / Redundancy: 16.2 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 2.7 / % possible all: 80.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J4W

2j4w


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.716 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R: 0.948 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAIN ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGENS RESIDUES A303 TO A477 AND A513 TO A545 ARE DISORDERED IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAIN ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGENS RESIDUES A303 TO A477 AND A513 TO A545 ARE DISORDERED IN THE CRYSTAL STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.278 847 5 %RANDOM
Rwork0.212 ---
obs0.215 16037 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.04 Å2
Baniso -1Baniso -2Baniso -3
1--6.02 Å2-3.01 Å20 Å2
2---6.02 Å20 Å2
3---9.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 0 0 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223713
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3861.9535056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9085470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18923.793145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.32615589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9411518
X-RAY DIFFRACTIONr_chiral_restr0.1460.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022807
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.21669
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.22485
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.74522423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05933836
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6143.51514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.71441220
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 63
Rwork0.371 1137

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more