[English] 日本語
Yorodumi
- PDB-4u0q: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u0q
TitlePlasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to basigin
Components
  • Basigin
  • Reticulocyte binding protein 5
KeywordsSIGNALING PROTEIN / Malaria Erythrocyte invasion
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / dendrite self-avoidance / response to mercury ion / cell-cell adhesion mediator activity / endothelial tube morphogenesis / neural retina development / Pyruvate metabolism ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / dendrite self-avoidance / response to mercury ion / cell-cell adhesion mediator activity / endothelial tube morphogenesis / neural retina development / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / homophilic cell adhesion via plasma membrane adhesion molecules / D-mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / response to cAMP / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / neutrophil chemotaxis / protein localization to plasma membrane / axon guidance / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Rh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Rh5 coiled-coil domain / Rh5 coiled-coil domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Reticulocyte binding protein 5 / Basigin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
CitationJournal: Nature / Year: 2014
Title: Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies.
Authors: Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Illingworth, J.J. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Dec 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reticulocyte binding protein 5
B: Basigin
C: Reticulocyte binding protein 5
D: Basigin


Theoretical massNumber of molelcules
Total (without water)184,7684
Polymers184,7684
Non-polymers00
Water00
1
A: Reticulocyte binding protein 5
B: Basigin


Theoretical massNumber of molelcules
Total (without water)92,3842
Polymers92,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area24740 Å2
MethodPISA
2
C: Reticulocyte binding protein 5
D: Basigin


Theoretical massNumber of molelcules
Total (without water)92,3842
Polymers92,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-6 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.280, 109.360, 151.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Reticulocyte binding protein 5 / Reticulocyte-binding protein homologue 5 / RH5


Mass: 63128.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B2L3N7
#2: Protein Basigin / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 29254.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / References: UniProt: P35613

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulphate, 20% PEG 4000, 0.1M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.1→67.46 Å / Num. obs: 23402 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 66.77 Å2 / Net I/σ(I): 9.4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0R, 3B5H

4u0r

3b5h


Resolution: 3.1→62.4 Å / Cor.coef. Fo:Fc: 0.8838 / Cor.coef. Fo:Fc free: 0.8393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.424
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1186 5.08 %RANDOM
Rwork0.2171 ---
obs0.2186 23357 99.68 %-
Displacement parametersBiso mean: 50.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.968 Å20 Å20 Å2
2--13.0382 Å20 Å2
3----11.0702 Å2
Refine analyzeLuzzati coordinate error obs: 0.631 Å
Refinement stepCycle: 1 / Resolution: 3.1→62.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 0 0 7629
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087793HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0610495HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2825SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes214HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1083HARMONIC5
X-RAY DIFFRACTIONt_it7793HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion21.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1029SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8500SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.24 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3156 145 5.18 %
Rwork0.2608 2654 -
all0.2636 2799 -
obs--99.68 %
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)
10.85821.3928-0.03164.01360.17360.28470.2651-0.1747-0.03740.5315-0.27060.03090.019-0.03410.0055-0.0212-0.07860.0048-0.06290.0623-0.094636.6471-5.7551-12.5209
21.6032-1.4204-1.42773.45640.93841.9702-0.02330.15350.0644-0.0187-0.00060.35010.0176-0.07040.0239-0.2641-0.0742-0.0336-0.15520.02650.113710.3552-26.2187-22.8114
30.6936-0.4424-0.23062.19330.43470.56860.0861-0.06040.0463-0.1356-0.04490.0388-0.104-0.0287-0.0411-0.10780.01990.0366-0.04460.0002-0.014513.15075.9789-42.2214
41.65091.0881-1.08963.6525-0.22911.3596-0.0742-0.2750.09690.54420.1174-0.0744-0.00430.2547-0.0432-0.03510.040.1116-0.1271-0.0407-0.201414.393420.1544-8.5105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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://pdbjlvh1.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