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- PDB-4u0q: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -

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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 / dendrite self-avoidance / acrosomal membrane / cell-cell adhesion mediator activity / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / dendrite self-avoidance / acrosomal membrane / cell-cell adhesion mediator activity / endothelial tube morphogenesis / response to mercury ion / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / D-mannose binding / homophilic cell-cell adhesion / odontogenesis of dentin-containing tooth / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / response to cAMP / Integrin cell surface interactions / Degradation of the extracellular matrix / neutrophil chemotaxis / photoreceptor inner segment / embryo implantation / positive regulation of endothelial cell migration / axon guidance / protein localization to plasma membrane / response to peptide hormone / sarcolemma / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / angiogenesis / basolateral plasma membrane / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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|* }

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