[English] 日本語
Yorodumi
- PDB-3zwz: Crystal structure of Plasmodium falciparum AMA1 in complex with a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zwz
TitleCrystal structure of Plasmodium falciparum AMA1 in complex with a 39aa PfRON2 peptide
Components
  • APICAL MEMBRANE ANTIGEN 1, AMA1
  • RHOPTRY NECK PROTEIN 2
KeywordsIMMUNE SYSTEM / MALARIA / MOVING JUNCTION
Function / homology
Function and homology information


rhoptry neck / apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1 / Rhoptry neck protein 2
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVulliez-Le Normand, B. / Tonkin, M.L. / Lamarque, M.H. / Langer, S. / Hoos, S. / Roques, M. / Saul, F.A. / Faber, B.W. / Bentley, G.A. / Boulanger, M.J. / Lebrun, M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural and Functional Insight Into the Malaria Parasite Moving Junction Complex
Authors: Vulliez-Le Normand, B. / Tonkin, M.L. / Lamarque, M.H. / Langer, S. / Hoos, S. / Roques, M. / Saul, F.A. / Faber, B.W. / Bentley, G.A. / Boulanger, M.J. / Lebrun, M.
History
DepositionAug 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN 1, AMA1
B: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9697
Polymers43,5092
Non-polymers4605
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-26.5 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.150, 38.260, 70.750
Angle α, β, γ (deg.)90.00, 99.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein APICAL MEMBRANE ANTIGEN 1, AMA1


Mass: 39443.336 Da / Num. of mol.: 1 / Fragment: DOMAINS I/II, RESIDUES 103-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q7KQK5
#2: Protein/peptide RHOPTRY NECK PROTEIN 2 / RON2


Mass: 4065.607 Da / Num. of mol.: 1 / Fragment: RESIDUES 2021-2059 / Source method: obtained synthetically
Source: (synth.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
References: UniProt: Q8IKV6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.9 % / Description: NONE
Crystal growDetails: 30% PEG400, 100 MM TRIS-HCL PH 8.5, 200 MM TRI-SODIUM CITRATE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→45.41 Å / Num. obs: 22041 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8V

2z8v


Resolution: 2.1→34.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.112 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20085 1127 5.1 %RANDOM
Rwork0.16388 ---
obs0.16583 20881 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.02 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 30 226 2892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9553699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55125.373134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212098
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2621.51664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14522693
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4631067
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.354.51006
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 74 -
Rwork0.202 1528 -
obs--99.94 %

+
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