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- PDB-2kve: C-terminal domain of mesencephalic astrocyte-derived neurotrophic... -

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Basic information

Entry
Database: PDB / ID: 2kve
TitleC-terminal domain of mesencephalic astrocyte-derived neurotrophic factor (MANF)
ComponentsMesencephalic astrocyte-derived neurotrophic factor
KeywordsHORMONE / Disulfide bond / Glycoprotein / Growth factor / Secreted / Sialic acid / Unfolded protein response
Function / homology
Function and homology information


vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / sarcoplasmic reticulum lumen / dopaminergic neuron differentiation / response to unfolded protein / growth factor activity / neuron projection development / Platelet degranulation / endoplasmic reticulum lumen ...vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / sarcoplasmic reticulum lumen / dopaminergic neuron differentiation / response to unfolded protein / growth factor activity / neuron projection development / Platelet degranulation / endoplasmic reticulum lumen / endoplasmic reticulum / RNA binding / extracellular space / extracellular region / nucleus / cytosol
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mesencephalic astrocyte-derived neurotrophic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, simulated annealing, TORSION ANGLE DYNAMICS
Model detailsfewest violations, model 1
AuthorsHellman, M.H. / Saarma, M. / Permi, P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mesencephalic Astrocyte-derived Neurotrophic Factor (MANF) Has a Unique Mechanism to Rescue Apoptotic Neurons
Authors: Hellman, M.H. / Arumae, U. / Yu, L.-Y. / Lindholm, P. / Peranen, J. / Saarma, M. / Permi, P.
History
DepositionMar 12, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mesencephalic astrocyte-derived neurotrophic factor


Theoretical massNumber of molelcules
Total (without water)7,4771
Polymers7,4771
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)15 / 400structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Mesencephalic astrocyte-derived neurotrophic factor / MANF / Protein ARMET / Arginine-rich protein


Mass: 7476.777 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP Residues 117-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: P55145
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C-CT-HSQC
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1812D (HB)CB(CGCD)HD
1912D (HB)CB(CGCDCE)HE
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] C-MANF; 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: C-MANF-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUNITY INOVA6001
Varian Unity InovaVarianUNITY INOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.26P.GUNTERT ET AL.automated noe assignment
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, simulated annealing, TORSION ANGLE DYNAMICS
Software ordinal: 1
NMR constraintsNOE constraints total: 845 / NOE intraresidue total count: 272 / NOE long range total count: 141 / NOE medium range total count: 217 / NOE sequential total count: 215
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 15 / Representative conformer: 1

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