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- PDB-2m7f: The C-terminal Region of Disintegrin Modulate its 3D Conformation... -

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Basic information

Entry
Database: PDB / ID: 2m7f
TitleThe C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Integrins Recognitions
ComponentsZinc metalloproteinase/disintegrin
KeywordsHYDROLASE / Rhodostomin mutant protein / RGD motif / C-terminal region mutation
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. ...Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model8
AuthorsChuang, W. / Chang, Y.
CitationJournal: To be Published
Title: The C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Recognitions of Integrins
Authors: Chuang, W. / Chang, Y. / Shiu, J. / Chen, C. / Chen, Y.
History
DepositionApr 22, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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: Zinc metalloproteinase/disintegrin


Theoretical massNumber of molelcules
Total (without water)8,6961
Polymers8,6961
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Zinc metalloproteinase/disintegrin / Snake venom metalloproteinase rhodostoxin / SVMP / Hemorrhagic protein / Disintegrin rhodostomin / ...Snake venom metalloproteinase rhodostoxin / SVMP / Hemorrhagic protein / Disintegrin rhodostomin / RHO / Disintegrin kistrin / Platelet aggregation activation inhibitor


Mass: 8695.713 Da / Num. of mol.: 1 / Fragment: UNP residues 408-478 / Mutation: P48A,M52W,P53N,Y67N,H68G,S69L,H70Y,A71G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Production host: Komagataella pastoris (fungus)
References: UniProt: P30403, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
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-1H NOESY
1212D 1H-1H TOCSY
1322D 1H-1H NOESY
1422D 1H-1H TOCSY
1533D 1H-15N NOESY
1633D 1H-15N TOCSY
1733D HNHA
1832D 1H-15N HSQC
1942D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM 2mM Rhodostomin 48ARGDWN-67NGLYG mutant-1, 90% H2O/10% D2O90% H2O/10% D2O
22 mM 2mM Rhodostomin 48ARGDWN-67NGLYG mutant-2, 100% D2O100% D2O
32 mM [U-15N] 2mM Rhodostomin 48ARGDWN-67NGLYG mutant-3, 90% H2O/10% D2O90% H2O/10% D2O
42 mM [U-15N] 2mM Rhodostomin 48ARGDWN-67NGLYG mutant-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mM2mM Rhodostomin 48ARGDWN-67NGLYG mutant-11
2 mM2mM Rhodostomin 48ARGDWN-67NGLYG mutant-22
2 mM2mM Rhodostomin 48ARGDWN-67NGLYG mutant-3[U-15N]3
2 mM2mM Rhodostomin 48ARGDWN-67NGLYG mutant-4[U-15N]4
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
AURELIA3.1.7Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerdata analysis
X-PLOR3.185Brungerrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 8

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