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- PDB-1peh: NMR STRUCTURE OF THE MEMBRANE-BINDING DOMAIN OF CTP PHOSPHOCHOLIN... -

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Basic information

Entry
Database: PDB / ID: 1peh
TitleNMR STRUCTURE OF THE MEMBRANE-BINDING DOMAIN OF CTP PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE, 10 STRUCTURES
ComponentsPEPNH1
KeywordsNUCLEOTIDYLTRANSFERASE / TRANSFERASE / PHOSPHOLIPID BIOSYNTHESIS / MEMBRANE / PHOSPHORYLATION
Function / homology
Function and homology information


Synthesis of PC / CDP-choline pathway / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / isotype switching / extrinsic component of membrane / molecular function inhibitor activity ...Synthesis of PC / CDP-choline pathway / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / isotype switching / extrinsic component of membrane / molecular function inhibitor activity / B cell proliferation / nuclear envelope / calmodulin binding / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Choline-phosphate cytidylyltransferase Pcy1-like / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Choline-phosphate cytidylyltransferase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / RESTRAINED DISTANCE GEOMETRY
AuthorsDunne, S.J. / Cornell, R.B. / Johnson, J.E. / Glover, N.R. / Tracey, A.S.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure of the membrane binding domain of CTP:phosphocholine cytidylyltransferase.
Authors: Dunne, S.J. / Cornell, R.B. / Johnson, J.E. / Glover, N.R. / Tracey, A.S.
#1: Journal: Biochemistry / Year: 1994
Title: Membrane-Binding Amphipathic Alpha-Helical Peptide Derived from Ctp:Phosphocholine Cytidylyltransferase
Authors: Johnson, J.E. / Cornell, R.B.
History
DepositionJun 10, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _entity.src_method / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_spectrometer.field_strength
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPNH1


Theoretical massNumber of molelcules
Total (without water)4,1491
Polymers4,1491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area270 Å2
ΔGint1 kcal/mol
Surface area4230 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
Representative

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Components

#1: Protein/peptide PEPNH1 / CYTIDYLYLTRANSFERASE MEMBRANE BINDING DOMAIN PEPTIDE


Mass: 4148.823 Da / Num. of mol.: 1 / Fragment: RESIDUES 236 - 268 / Mutation: F263W / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P19836, choline-phosphate cytidylyltransferase
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Sample conditionspH: 5.2 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DGIIBIOSYMrefinement
BIOSYM MOLECULAR SIMULATIONS/FELIXSIMULATIONS/FELIXstructure solution
RefinementMethod: RESTRAINED DISTANCE GEOMETRY / Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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