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- PDB-2jsf: Solution structures of the envelope protein domain III from the d... -

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Basic information

Entry
Database: PDB / ID: 2jsf
TitleSolution structures of the envelope protein domain III from the dengue-2 virus
Componentsdomain III of ENVELOPE PROTEIN E
KeywordsVIRAL PROTEIN / Domain III
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDengue virus
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, K. / Cheng, J.
CitationJournal: Proteins / Year: 2008
Title: Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein.
Authors: Huang, K.C. / Lee, M.C. / Wu, C.W. / Huang, K.J. / Lei, H.Y. / Cheng, J.W.
History
DepositionJul 3, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: domain III of ENVELOPE PROTEIN E


Theoretical massNumber of molelcules
Total (without water)13,2821
Polymers13,2821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein domain III of ENVELOPE PROTEIN E


Mass: 13282.361 Da / Num. of mol.: 1 / Fragment: Residues 469-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus / Genus: Flavivirus / Strain: 2 / Plasmid: pET-Blue2 / Production host: Escherichia coli (E. coli) / References: UniProt: P18356

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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
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D H(CCO)NH
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D HNCA

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Sample preparation

DetailsContents: 1-5 mM EDTA, 1-5 mM DTT, 1 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMEDTA1
1 mMDTT1
1 mMsodium azide1
Sample conditionsIonic strength: 0.31 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SPARKYGoddarddata analysis
XWINNMRBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxcollection
ProcheckNMRLaskowski and MacArthurdata analysis
MolmolKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: 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: 100 / Conformers submitted total number: 20

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