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- PDB-9fp9: Three-dimensional structure of the Merozoite surface protein 1 C-... -

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Basic information

Entry
Database: PDB / ID: 9fp9
TitleThree-dimensional structure of the Merozoite surface protein 1 C-terminal domain
ComponentsMerozoite surface protein 1
KeywordsMEMBRANE PROTEIN / Malaria / Plasmodium berghei / EGF-domain / dynamic N-terminus
Function / homologyMerozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / side of membrane / extracellular region / plasma membrane / Merozoite surface protein 1
Function and homology information
Biological speciesPlasmodium berghei (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsBier, N. / Ramadan, S. / Nedielkov, R. / Klishin, N. / Moeller, H.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck SocietyIMPRS Multiscale Biosystems Germany
CitationJournal: To Be Published
Title: Three-dimensional structure of the Merozoite surface protein 1 C-terminal domain from P. berghei
Authors: Bier, N. / Ramadan, S. / Nedielkov, R. / Klishin, N. / Moeller, H.M.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)11,4611
Polymers11,4611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Merozoite surface protein 1 / Merozoite surface antigen / PMMSA


Mass: 11460.739 Da / Num. of mol.: 1 / Mutation: M1, G104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: MSP1, PBNK65NY_000166300 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C6YE36
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CO
1101isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D HBHA(CO)NH
171isotropic13D HBHANH
161isotropic13D 1H-15N NOESY
1131isotropic13D 1H-15N TOCSY
1111isotropic13D H(CCO)NH
1161isotropic13D C(CO)NH
2152isotropic13D (H)CCH-COSY
2142isotropic13D (H)CCH-TOCSY
2122isotropic12D 1H-1H NOESY
2172isotropic13D 1H-13C NOESY aliphatic
2182isotropic1(HB)CB(CGCD)HD
2192isotropic1(HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.873 mM [U-99% 13C; U-98% 15N] MSP1-19, 25 mM Potassium dihydrogen phosphate, 50 mM Potassium chloride, 4 mM Sodium azide, 0.1 mM d6 DSS, 95% H2O/5% D2O15N,13C_sample95% H2O/5% D2O
solution20.741 mM [U-99% 13C; U-98% 15N] MSP1-19, 25 mM Potassium dideuterium phosphate, 50 mM Potassium chloride, 4 mM Sodium azide, 0.1 mM d6 DSS, 100% D2O15N,13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.873 mMMSP1-19[U-99% 13C; U-98% 15N]1
25 mMPotassium dihydrogen phosphatenone1
50 mMPotassium chloridenone1
4 mMSodium azidenone1
0.1 mMDSSd61
0.741 mMMSP1-19[U-99% 13C; U-98% 15N]2
25 mMPotassium dideuterium phosphatenone2
50 mMPotassium chloridenone2
4 mMSodium azidenone2
0.1 mMDSSd62
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1187.5 mMMSP1-19 in water6.51 atm298 K
2187.5 mMMSP1-19 in deuterium oxide6.5 pD1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: Prodigy cryo-probe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
ARTINAKlukowski, P., Riek, R. and Guntert, P.structure calculation
CYANA3.98.15Guntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics5
simulated annealing2with explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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