[English] 日本語
Yorodumi
- PDB-3n42: Crystal structures of the mature envelope glycoprotein complex (f... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3n42
TitleCrystal structures of the mature envelope glycoprotein complex (furin cleavage) of Chikungunya virus.
DescriptorE3 envelope glycoprotein
E2 envelope glycoprotein
E1 envelope glycoprotein
KeywordsVIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION
Specimen sourceChikungunya virus / virus / CHIKV / チクングニヤウイルス
MethodX-ray diffraction (3 Å resolution / Molecular replacement)
AuthorsVoss, J. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
CitationNature, 2010, 468, 709-712

primary. Nature, 2010, 468, 709-712 Yorodumi Papers
Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
Voss, J.E. / Vaney, M.C. / Duquerroy, S. / Vonrhein, C. / Girard-Blanc, C. / Crublet, E. / Thompson, A. / Bricogne, G. / Rey, F.A.

#1. Structure, 2006, 14, 75-86 Yorodumi Papers
Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus.
Roussel, A. / Lescar, J. / Vaney, M.C. / Wengler, G. / Rey, F.A.

#2. Nature, 2004, 427, 320-325 Yorodumi Papers
Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.
Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A.

#3. Cell(Cambridge,Mass.), 2001, 105, 137-148 Yorodumi Papers
The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH.
Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Rey, F.A.

#4. To be Published Search PubMed
Structural Changes of Envelope Proteins During Alphavirus Fusion.
Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2010 / Release: Dec 1, 2010
RevisionDateData content typeGroupProviderType
1.0Dec 1, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: E3 envelope glycoprotein
B: E2 envelope glycoprotein
F: E1 envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0916
Polyers98,4283
Non-polymers6643
Water1,58588
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7690
ΔGint (kcal/M)-21
Surface area (Å2)37660
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.391, 90.678, 178.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

-
Polypeptide(L) , 3 types, 3 molecules ABF

#1: Polypeptide(L)E3 envelope glycoprotein


Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 266-319 / Source: (gene. exp.) Chikungunya virus / References: UniProt: Q1H8W5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)
#2: Polypeptide(L)E2 envelope glycoprotein


Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 330-667 / Source: (gene. exp.) Chikungunya virus / References: UniProt: Q1H8W5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)
#3: Polypeptide(L)E1 envelope glycoprotein


Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1202 / Source: (gene. exp.) Chikungunya virus / References: UniProt: Q1H8W5

Cellular component

Molecular function

Biological process

  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)

-
Non-polymers , 3 types, 91 molecules

#4: ChemicalChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6
#5: ChemicalChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#6: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Formula: H2O

-
Details

Sequence detailsTHE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPSIN BEFORE CRYSTALLIZATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 / Density percent sol: 48.74
Crystal growTemp: 293 K / pH: 7
Details: 8-12% PEG4K, 100mM NaAcetate, 100mM Hepes pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID23-2 / Synchrotron site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD
Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
Detector: CCD / Collection date: Nov 13, 2009
RadiationMonochromator: S 111 / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 68.11 Å2 / D resolution high: 3 Å / D resolution low: 49.7 Å / Number obs: 18964 / Observed criterion sigma I: 0 / Rsym value: 0.123 / NetI over sigmaI: 9.2 / Redundancy: 3.7 / Percent possible obs: 96.4
Reflection shellHighest resolution: 3 Å / Lowest resolution: 3.16 Å / MeanI over sigI obs: 2 / Rsym value: 0.469 / Redundancy: 2.4 / Percent possible all: 82.2

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS

Correlation coeff Fo to Fc: 0.85 / Correlation coeff Fo to Fc free: 0.832 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso mean: 59.22 Å2 / Aniso B11: -0.5004 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 13.0951 Å2 / Aniso B23: 0 Å2 / Aniso B33: -12.5948 Å2
Least-squares processR factor R free: 0.278 / R factor R work: 0.247 / R factor obs: 0.249 / Highest resolution: 3 Å / Lowest resolution: 44.6 Å / Number reflection R free: 980 / Number reflection obs: 18926 / Percent reflection R free: 5.18 / Percent reflection obs: 96.2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 44.6 Å
Number of atoms included #LASTProtein: 6075 / Nucleic acid: 0 / Ligand: 42 / Solvent: 88 / Total: 6205
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076310HARMONIC2.000
X-RAY DIFFRACTIONt_angle_deg0.978613HARMONIC2.000
X-RAY DIFFRACTIONt_dihedral_angle_d2080SINUSOIDAL2.000
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes147HARMONIC2.000
X-RAY DIFFRACTIONt_gen_planes918HARMONIC5.000
X-RAY DIFFRACTIONt_it6310HARMONIC20.000
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.800
X-RAY DIFFRACTIONt_other_torsion19.340
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion847SEMIHARMONIC5.000
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6322SEMIHARMONIC4.000
Refine LS shellHighest resolution: 3 Å / R factor R free: 0.3655 / R factor R work: 0.3033 / R factor all: 0.3066 / Lowest resolution: 3.16 Å / Number reflection R free: 131 / Number reflection R work: 2172 / Number reflection all: 2303 / Total number of bins used: 10 / Percent reflection R free: 5.69 / Percent reflection obs: 96.15
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.2512-0.70560.14271.6013-0.27010.0000-0.00090.00980.0330-0.0057-0.00500.0402-0.0343-0.01990.0059-0.03950.0195-0.06320.0222-0.02130.1451-56.6176-12.9749-35.3159
22.44752.83890.69515.85401.47900.7329-0.0155-0.02440.01680.3762-0.06170.13070.0299-0.10150.07720.0705-0.02720.1492-0.1991-0.0639-0.0259-36.0388-15.8476-17.4125
34.72070.0425-1.03630.68780.40782.1543-0.00040.0315-0.0942-0.05140.0098-0.01860.12940.0091-0.0095-0.0193-0.11060.06470.02580.00710.0503-50.1963-45.5195-31.6189
43.9550-1.38932.89981.31932.23243.5027-0.0065-0.1200-0.00050.1034-0.0067-0.0478-0.01050.07040.01320.0037-0.0825-0.1399-0.0478-0.0366-0.0079-3.506713.0088-9.1447
51.19071.5837-0.07882.3282-0.48121.1425-0.0009-0.0174-0.0146-0.0443-0.01450.03220.05890.00420.0154-0.0349-0.0455-0.05730.00910.01930.0516-12.772136.0262-28.0040
62.39971.9330-0.81715.19032.27263.78290.00760.0344-0.0272-0.0537-0.0337-0.0719-0.0544-0.00970.0261-0.10140.0078-0.0941-0.04920.02370.0708-18.18911.3197-33.6945
71.9558-0.52151.46653.50351.83860.87610.0056-0.0397-0.0598-0.0297-0.00790.05360.0558-0.00900.0024-0.02670.01270.01130.0323-0.0279-0.0297-30.2185-29.0831-36.5390
80.0000-0.10130.18720.00000.03110.0000-0.0018-0.01440.01450.0115-0.00480.0011-0.01370.00180.0066-0.00330.0072-0.01010.0150-0.0205-0.0136-14.551459.9645-26.5908
91.54102.04362.34100.9723-0.86837.7003-0.0032-0.01510.01870.0320-0.0162-0.0010-0.12500.04050.01940.0986-0.0791-0.1466-0.0740-0.0282-0.1196-1.937748.9606-9.1154
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1{A|7:58}
2X-RAY DIFFRACTION2{B|5:169 233:268}
3X-RAY DIFFRACTION3{B|170:232}
4X-RAY DIFFRACTION4{B|269:342}
5X-RAY DIFFRACTION5{F|-1-39 127:171 255:281}
6X-RAY DIFFRACTION6{F|40:51 111:126 172:216 238:254}
7X-RAY DIFFRACTION7{F|52:110 217:237}
8X-RAY DIFFRACTION8{F|282:293}
9X-RAY DIFFRACTION9{F|294:393}

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more