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- PDB-1d8v: THE RESTRAINED AND MINIMIZED AVERAGE NMR STRUCTURE OF MAP30. -

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Basic information

Entry
Database: PDB / ID: 1d8v
TitleTHE RESTRAINED AND MINIMIZED AVERAGE NMR STRUCTURE OF MAP30.
ComponentsANTI-HIV AND ANTI-TUMOR PROTEIN MAP30
KeywordsANTITUMOR PROTEIN / SINGLE CHAIN
Function / homology
Function and homology information


regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-inactivating protein beta-momorcharin
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Y.-X. / Neamati, N. / Jacob, J. / Palmer, I. / Stahl, S.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions.
Authors: Wang, Y.X. / Neamati, N. / Jacob, J. / Palmer, I. / Stahl, S.J. / Kaufman, J.D. / Huang, P.L. / Huang, P.L. / Winslow, H.E. / Pommier, Y. / Wingfield, P.T. / Lee-Huang, S. / Bax, A. / Torchia, D.A.
History
DepositionOct 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI-HIV AND ANTI-TUMOR PROTEIN MAP30


Theoretical massNumber of molelcules
Total (without water)29,6311
Polymers29,6311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1

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Components

#1: Protein ANTI-HIV AND ANTI-TUMOR PROTEIN MAP30


Mass: 29630.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P24817

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1214D 13C/15N-SEPARATED NOESY
1313D 13C-SEPARATED NOESY
1414D 13C-SEPARATED NOESY
151HNHA
161HNCA-J
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING DIPOLAR COUPLING MEASURED IN LIQUID CRYSTAL MEDIA. IN ADDITION, WE ALSO MEASURED HYDROGEN BONDS DIRECTLY AND USED THEM IN STRUCTURE CALCULATIONS.

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Sample preparation

DetailsContents: ~0.7 MM PROTEIN MAP30 (15N/13C) ENRICHED.
Sample conditionsIonic strength: 10 mM NAPI / pH: 5.50 / Pressure: 1 atm / Temperature: 313.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
MODIFIED X-PLOR3.5BRUNGERrefinement
MODIFIED X-PLOR3.5BRUNGERstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: WE CALCULATED THE STRUCTURE OF MAP30 USING SIMULATED ANNEALING IN TORSION ANGLE SPACE STARTING FROM AN EXTENDED STRAND, FOLLOWED BY SIMULATED ANEALING IN CARTESIAN SPACE USING A MODIFIED ...Details: WE CALCULATED THE STRUCTURE OF MAP30 USING SIMULATED ANNEALING IN TORSION ANGLE SPACE STARTING FROM AN EXTENDED STRAND, FOLLOWED BY SIMULATED ANEALING IN CARTESIAN SPACE USING A MODIFIED XPLOR 3.5, CONTAINING PSEUDOPOTENTIALS FOR RESIDUAL DIPOLAR COUPLING AND A CONFORMATIONAL DATABASE. HYDROGEN BOND CONSTRAINTS, TWO FOR EACH HYDROGEN BOND (NH-O = 1.5-2.8 A AND N-O = 2.4-3.5 A), WERE DERIVED FROM NH EXCHANGE EXPERIMENTS, BACKBONE NOE PATTERNS, BACKBONE CA/CB CHEMICAL SHIFTS AND DIRECT MEASUREMENTS OF 3HJNC CONNECTIVITY ACROSS HYDROGEN BONDS, AND APPLIED IN THE LATER STAGE OF THE STRUCTURE CALCULATION. PHI AND PSI ANGLES WERE DERIVED FROM THREE-BOND 3JHNHA COUPLING CONSTANTS, MEASURED WITH THE 3D HNHA EXPERIMENT AND A DATABASE ANALYSIS OF BACKBONE (1H, 15N, 13CA, 13CB AND C) CHEMICAL SHIFTS, USING THE PROGRAM TALOS. THE PHI DIHEDRAL ANGLE WAS RESTRAINED TO -60 DEGREES PLUS-MINUS 30 DEGREES IF JHNHA < 5.5 HZ OR TO 110 DEGREES PLUS-MINUS 50 DEGREES IF JHNHA >8.0 HZ. CHI 1 DIHEDRAL ANGLES AND STEREOSPECIFIC ASSIGNMENTS OF BETA- METHYLENE PROTONS WERE DERIVED FROM JHNHB AND JHAHB SCALAR COUPLING CONSTANTS OBTAINED FROM 3D HNHB AND HACAHB-COSY EXPERIMENTS. TIGHT TURNS CLEARLY IDENTIFIED BY NOE PATTERNS AND J-COUPLING CONSTANTS, PHI AND PSI ANGLES WERE RESTRAINED TO THEIR STANDARD VALUES WITH PLUS-MINUS 30 DEGREES ERROR RANGE. FOR RESIDUES HAVING INTENSE INTRARESIDUE HN-HA NOES WITH POSITIVE PHI ANGLES SUGGESTED BY THE PROGRAM TALOS, PHI WAS RESTRAINED TO 40 DEGREES PLUS-MINUS 15 DEGREES. ELECTROSTATIC SURFACES WERE CALCULATED USING GRASP. MOLECULAR MODELS WERE GENERATED WITH QUANTA (MSI), INSIGHT (MSI) AND MOLSCRIPT.
NMR ensembleConformers submitted total number: 1

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