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- PDB-7s7q: Heterodimeric complex of Pf12 and Pf41 of Plasmodium falciparum -

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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
Immunoglobulin-like - #2860 / : / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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


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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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