[English] 日本語
Yorodumi
- PDB-7s7q: Heterodimeric complex of Pf12 and Pf41 of Plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s7q
TitleHeterodimeric complex of Pf12 and Pf41 of Plasmodium falciparum
Components
  • Merozoite surface protein P12
  • Merozoite surface protein P41
KeywordsUNKNOWN FUNCTION / 6-cysteine protein / s48/45 domain / complex / heterodimer
Function / homology
Function and homology information


symbiont-containing vacuolar space / symbiont entry into host / side of membrane / apical part of cell / cell surface / plasma membrane
Similarity search - Function
6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain
Similarity search - Domain/homology
: / Merozoite surface protein P12 / Merozoite surface protein P41
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2001385 United Kingdom
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: FEMS Microbes / Year: 2022
Title: Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins.
Authors: Dietrich, M.H. / Chan, L.J. / Adair, A. / Boulet, C. / O'Neill, M.T. / Tan, L.L. / Keremane, S. / Mok, Y.F. / Lo, A.W. / Gilson, P. / Tham, W.H.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Merozoite surface protein P41
B: Merozoite surface protein P12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,90411
Polymers71,6742
Non-polymers1,2299
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, analytical ultracentrifugation, binding and affinity determination using Bio-layer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-48 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.712, 73.712, 332.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Merozoite surface protein P41


Mass: 39932.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF41, PFD0240c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I1Y0
#2: Protein Merozoite surface protein P12


Mass: 31742.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF12, PFF0615c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KSX0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM cadmium chloride, 14% (w/v) PEG 4000, 25% glycerol, 50 mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953644 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953644 Å / Relative weight: 1
ReflectionResolution: 2.85→49.355 Å / Num. obs: 40863 / % possible obs: 99.7 % / Redundancy: 7.897 % / Biso Wilson estimate: 91.435 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.081 / Χ2: 0.832 / Net I/σ(I): 15.59 / Num. measured all: 322715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.85-3.027.9521.0441.5451351657964580.8491.11798.2
3.02-3.237.8320.5363.0148959625162510.9670.575100
3.23-3.487.7530.2696.0145067581358130.9880.288100
3.48-3.818.2990.14611.6943809527952790.9950.156100
3.81-4.268.1010.08919.4139168483548350.9980.096100
4.26-4.917.5470.06428.1432258427442740.9980.069100
4.91-67.9140.05633.6528373358535850.9980.06100
6-8.437.8920.04937.2822019279027900.9990.052100
8.43-49.3557.4210.03946.0711711159215780.9990.04199.1

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMO, 4YS4

2ymo

4ys4


Resolution: 2.85→47.16 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2016 4.95 %
Rwork0.2299 38725 -
obs0.2327 40741 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.15 Å2 / Biso mean: 116.4552 Å2 / Biso min: 54.41 Å2
Refinement stepCycle: final / Resolution: 2.85→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 34 0 4215
Biso mean--154.26 --
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054301
X-RAY DIFFRACTIONf_angle_d0.8075865
X-RAY DIFFRACTIONf_dihedral_angle_d3.2813023
X-RAY DIFFRACTIONf_chiral_restr0.051683
X-RAY DIFFRACTIONf_plane_restr0.006772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.85-2.92130.34751410.3397275799
2.9213-3.00030.35371450.31632761100
3.0003-3.08850.33141440.29482757100
3.0885-3.18820.38071440.3012765100
3.1882-3.30210.35281450.27272757100
3.3021-3.43430.34771370.27062776100
3.4343-3.59050.27611460.24822766100
3.5905-3.77980.30591480.24642751100
3.7798-4.01650.29771480.22222796100
4.0165-4.32640.31931500.2062767100
4.3264-4.76140.24131420.1842750100
4.7614-5.44950.23121460.1882774100
5.4495-6.86240.28331430.23762782100
6.8624-47.160.27711370.23352766100
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)
13.69860.5760.38172.7864-0.12224.7690.1252-0.18470.9698-0.2796-0.0277-0.5242-0.11972.1455-0.13710.6291-0.06-0.0781.7354-0.13661.3968.42425.2567-26.7475
26.9768-0.58980.4994.4121-0.33066.9866-0.0588-0.75790.23190.3933-0.56610.437-1.43961.27030.7930.9972-0.35930.11261.1469-0.00961.2177-7.836118.0842-24.6464
33.562-0.15330.14633.31540.71073.46180.01270.0492-0.04250.2308-0.126-0.63210.62461.2356-0.00490.77460.2415-0.13731.40120.02240.9222.6063-3.3337-31.0034
44.7081-0.4574-0.1612.5741.38435.259-0.31220.0655-0.40880.49890.071-0.44251.43490.36840.14431.04270.09020.08360.6133-0.01860.8251-13.5936-11.0094-32.3547
53.12960.17110.34651.587-1.56131.68520.3494-0.8033-1.08190.3877-0.8506-0.32571.7826-0.24390.33551.464-0.43360.35121.0186-0.02190.8405-41.4707-15.0822-5.5291
65.27873.3045-0.66826.378-5.36555.8914-0.39621.1899-3.0167-2.26010.0702-1.1251.5734-0.3166-0.50552.6002-0.75720.48230.8877-0.34640.5573-40.262-15.3809-17.0256
72.79881.0744-0.34912.30480.51753.2874-0.37520.21710.1354-1.18730.47510.29880.0448-0.18280.0580.9599-0.24790.13330.62770.02780.8242-39.171-3.2826-14.832
80.23250.4203-0.38260.0558-0.0031-0.07960.16040.4837-0.0160.76770.01870.28221.4813-1.5612-0.1561.9839-0.80510.21330.96090.10360.9926-50.6356-16.8998-12.9212
91.35712.2051-1.74323.0603-1.37351.72220.233-0.32630.38950.25720.21240.7149-0.0744-1.2755-0.34470.7448-0.27020.14060.8851-0.0090.8046-34.609211.8649-11.0348
102.69721.2781.33943.25310.02534.34720.22030.04070.41890.4598-1.0143-0.2308-0.61961.01020.64550.8584-0.15590.06190.71320.03490.7914-22.651516.1934-19.3837
113.7111-1.5923-0.91361.75111.07342.5276-0.4584-0.2358-1.07990.0208-0.1812-1.7241.30530.17870.35151.1319-0.03770.05671.3337-0.01891.3229-10.337710.1225-10.8863
122.5365-0.8263-2.75762.86961.54744.2897-0.3641-0.5727-0.91260.3271-0.8244-0.16180.00650.6931.00010.6882-0.19640.09490.65350.00270.7893-24.81144.4605-14.2347
132.9485-0.761-0.26662.05180.16983.47560.2874-0.2008-0.0131-0.06420.1096-0.7122-0.24310.8191-0.17880.8474-0.28870.03481.0327-0.03871.0097-16.829615.5505-12.5519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 151 )A20 - 151
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 178 )A152 - 178
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 261 )A179 - 261
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 368 )A262 - 368
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 66 )B28 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 83 )B67 - 83
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 131 )B84 - 131
8X-RAY DIFFRACTION8chain 'B' and (resid 132 through 162 )B132 - 162
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 194 )B163 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 237 )B195 - 237
11X-RAY DIFFRACTION11chain 'B' and (resid 238 through 257 )B238 - 257
12X-RAY DIFFRACTION12chain 'B' and (resid 258 through 271 )B258 - 271
13X-RAY DIFFRACTION13chain 'B' and (resid 272 through 303 )B272 - 303

+
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