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- PDB-2hp8: SOLUTION STRUCTURE OF HUMAN P8-MTCP1, A CYSTEINE-RICH PROTEIN ENC... -

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Basic information

Entry
Database: PDB / ID: 2hp8
TitleSOLUTION STRUCTURE OF HUMAN P8-MTCP1, A CYSTEINE-RICH PROTEIN ENCODED BY THE MTCP1 ONCOGENE,REVEALS A NEW ALPHA-HELICAL ASSEMBLY MOTIF, NMR, 30 STRUCTURES
ComponentsCx9C motif-containing protein 4
KeywordsCYSTEINE MOTIF / HU-P8 / LEUKEMIA
Function / homology
Function and homology information


Mitochondrial protein import / mitochondrial intermembrane space / mitochondrion
Similarity search - Function
Mature-T-Cell Proliferation I type / Mature-T-Cell Proliferation I type / CytochromE C oxidase copper chaperone / Cysteine alpha-hairpin motif superfamily / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cx9C motif-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsBarthe, P. / Chiche, L. / Strub, M.P. / Roumestand, C.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of human p8MTCP1, a cysteine-rich protein encoded by the MTCP1 oncogene, reveals a new alpha-helical assembly motif.
Authors: Barthe, P. / Yang, Y.S. / Chiche, L. / Hoh, F. / Strub, M.P. / Guignard, L. / Soulier, J. / Stern, M.H. / van Tilbeurgh, H. / Lhoste, J.M. / Roumestand, C.
#1: Journal: Oncogene / Year: 1994
Title: The Mtcp-1/C6.1B Gene Encodes for a Cytoplasmic 8 Kd Protein Overexpressed in T Cell Leukemia Bearing a T(X;14) Translocation
Authors: Soulier, J. / Madani, A. / Cacheux, V. / Rosenzwajg, M. / Sigaux, F. / Stern, M.H.
#2: Journal: Oncogene / Year: 1993
Title: Mtcp-1: A Novel Gene on the Human Chromosome Xq28 Translocated to the T Cell Receptor Alpha/Delta Locus in Mature T Cell Proliferations
Authors: Stern, M.H. / Soulier, J. / Rosenzwajg, M. / Nakahara, K. / Canki-Klain, N. / Aurias, A. / Sigaux, F. / Kirsch, I.R.
History
DepositionAug 26, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 21, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_refine.details / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model / _struct.pdbx_descriptor / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cx9C motif-containing protein 4


Theoretical massNumber of molelcules
Total (without water)8,8891
Polymers8,8891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4340 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30structures with the least restraint violations
Representative

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Components

#1: Protein Cx9C motif-containing protein 4 / Mature T-cell proliferation 1 neighbor protein / Mature T-cell proliferation-1 type A / MTCP-1 type ...Mature T-cell proliferation 1 neighbor protein / Mature T-cell proliferation-1 type A / MTCP-1 type A / Protein p8 MTCP-1 / p8MTCP1


Mass: 8889.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cellular location: MITOCHONDRIA / Gene: CMC4, C6.1B, MTCP1, MTCP1NB / Plasmid: PGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56277
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY

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Sample preparation

Sample conditionsIonic strength: 10mM PO4 mM / Label: sample conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
UXNMRstructure solution
Gifastructure solution
DIANAP. GUNTERT AND K. WUTHRICHstructure solution
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE 3D STRUCTURE OF P8-MTCP1 IN SOLUTION BY NMR IS BASED ON 931 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS AND 57 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT ...Details: THE 3D STRUCTURE OF P8-MTCP1 IN SOLUTION BY NMR IS BASED ON 931 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS AND 57 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT MEASUREMENTS. THE STRUCTURES ARE CALCULATED USING THE DISTANCE GEOMETRY DIANA METHOD AND REFINED USING A SIMULATED-ANNEALING PROTOCOL WITH THE PROGRAM AMBER 4.1.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 30

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