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- PDB-2lkl: Structure of the core intracellular domain of PfEMP1 -

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Basic information

Entry
Database: PDB / ID: 2lkl
TitleStructure of the core intracellular domain of PfEMP1
ComponentsErythrocyte membrane protein 1 (PfEMP1)Red blood cell
KeywordsCELL ADHESION / Helical protein
Function / homologyAcidic terminal segments, variant surface antigen of PfEMP1 / c-terminal domain of poly(a) binding protein / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model 1
AuthorsVakonakis, I. / Erat, M.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Analysis of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Intracellular Domain Reveals a Conserved Interaction Epitope.
Authors: Mayer, C. / Slater, L. / Erat, M.C. / Konrat, R. / Vakonakis, I.
History
DepositionOct 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythrocyte membrane protein 1 (PfEMP1)


Theoretical massNumber of molelcules
Total (without water)9,7231
Polymers9,7231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)39 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Erythrocyte membrane protein 1 (PfEMP1) / Red blood cell


Mass: 9722.960 Da / Num. of mol.: 1 / Fragment: ATS-Core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Description: Modified pET16b vector with 3C-protease site / Gene: var / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The structured core of the intracellular domain of PfEMP1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1623D HN(CA)CB
1723D H(CCO)NH
1833D (H)CCH-COSY
1913D HNHB
11013D HNHA
11133D 1H-13C NOESY
11213D 1H-15N NOESY
11323D HBHA(CO)NH
11434D 13C-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] ATS-Core, 95 % H2O, 5 % [U-2H] D2O, 1 mM DTT, 0.1 mM DSS, 20 mM sodium phosphate, 50 mM sodium chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-13C; U-15N] ATS-Core, 95 % H2O, 5 % [U-2H] D2O, 1 mM DTT, 0.1 mM DSS, 20 mM sodium phosphate, 50 mM sodium chloride, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-13C; U-15N] ATS-Core, 100 % [U-2H] D2O, 1 mM DTT, 0.1 mM DSS, 20 mM sodium phosphate, 50 mM sodium chloride, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMATS-Core-1[U-100% 15N]1
95 %H2O-21
5 %D2O-3[U-2H]1
1 mMDTT-41
0.1 mMDSS-51
20 mMsodium phosphate-61
50 mMsodium chloride-71
0.01 %sodium azide-81
1 mMATS-Core-9[U-13C; U-15N]2
95 %H2O-102
5 %D2O-11[U-2H]2
1 mMDTT-122
0.1 mMDSS-132
20 mMsodium phosphate-142
50 mMsodium chloride-152
0.01 %sodium azide-162
1 mMATS-Core-17[U-13C; U-15N]3
100 %D2O-18[U-2H]3
1 mMDTT-193
0.1 mMDSS-203
20 mMsodium phosphate-213
50 mMsodium chloride-223
0.01 %sodium azide-233
Sample conditionsIonic strength: 0.11 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
home built OMEGAHome-builtOMEGA6002
home built OMEGAHome-builtOMEGA5003
home built OMEGAHome-builtOMEGA9504

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4 Rev 2006.095.11.35Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPP4.3.7Garrettchemical shift assignment
Omega_Spectrometer_Operating_SoftwareBeta 6.03b2GE/Brukercollection
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1147 / NOE intraresidue total count: 383 / NOE long range total count: 196 / NOE medium range total count: 310 / NOE sequential total count: 256
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.46 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 39 / Maximum lower distance constraint violation: 0.3 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.0208 Å / Distance rms dev error: 0.0017 Å

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