[English] 日本語
Yorodumi
- PDB-3uze: Crystal structure of the dengue virus serotype 3 envelope protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uze
TitleCrystal structure of the dengue virus serotype 3 envelope protein domain III in complex with the variable domains of Mab 4E11
Components
  • Envelope protein
  • Variable domains of murine anti-dengue Mab 4E11
KeywordsIMMUNE SYSTEM / dengue antibody neutralization
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dengue virus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCockburn, J.J.B. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A.
CitationJournal: Structure / Year: 2012
Title: Mechanism of dengue virus broad cross-neutralization by a monoclonal antibody.
Authors: Cockburn, J.J. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Variable domains of murine anti-dengue Mab 4E11
B: Variable domains of murine anti-dengue Mab 4E11
C: Envelope protein
D: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,67115
Polymers84,6624
Non-polymers1,00911
Water4,990277
1
A: Variable domains of murine anti-dengue Mab 4E11
C: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7948
Polymers42,3312
Non-polymers4626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Variable domains of murine anti-dengue Mab 4E11
D: Envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8787
Polymers42,3312
Non-polymers5475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.055, 74.670, 86.888
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody / Protein , 2 types, 4 molecules ABCD

#1: Antibody Variable domains of murine anti-dengue Mab 4E11


Mass: 27246.186 Da / Num. of mol.: 2 / Fragment: Single chain variable fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#2: Protein Envelope protein


Mass: 15084.850 Da / Num. of mol.: 2 / Fragment: domain III (UNP residues 293-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 3 / Strain: Thailand/PaH881/1988 / Gene: E / Plasmid: pT351 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q7TGD1, UniProt: P27915*PLUS

-
Non-polymers , 4 types, 288 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0721 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2008 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.037→42.857 Å / Num. all: 40602 / Num. obs: 40602 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.084 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.04-2.152.50.4441.71168747500.44476
2.15-2.283.50.36221978356770.36296.9
2.28-2.433.70.24932046655070.24998.8
2.43-2.633.60.1774.21822050740.17798.7
2.63-2.883.80.1216.11776847160.12198.9
2.88-3.223.60.0848.11526542200.08498.2
3.22-3.723.80.063101419137280.06398.5
3.72-4.553.70.05211.51169131660.05298
4.55-6.443.70.04812.2903724220.04897.2
6.44-42.8573.80.04312.7510813420.04395.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
BUSTER2.9.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UZG, 3UZQ

1uzg

3uzq


Resolution: 2.04→40.8 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9185 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1981 4.9 %RANDOM
Rwork0.2177 ---
all0.2185 40459 --
obs0.2185 40459 94.62 %-
Displacement parametersBiso max: 127.94 Å2 / Biso mean: 37.2848 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.8499 Å20 Å22.2582 Å2
2--2.1541 Å20 Å2
3---0.6959 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: LAST / Resolution: 2.04→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 65 277 5158
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1734SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it5032HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion665SEMIHARMONIC5
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_contact5605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5032HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg6813HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion15.57
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2504 98 4.41 %
Rwork0.2281 2126 -
all0.2291 2224 -
obs--94.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.36730.03640.42361.22860.24721.6562-0.02250.0648-0.04250.11550.01660.0254-0.00720.05120.0059-0.0328-0.0269-0.0162-0.0641-0.0129-0.023926.877-15.405115.5203
22.04330.34160.41392.54160.05181.313-0.01240.261-0.1263-0.09480.02340.14770.00250.0648-0.011-0.0871-0.0111-0.0161-0.0524-0.0373-0.027111.0177-23.74573.0979
31.20970.39060.40621.9761-0.18532.24260.0123-0.11830.14040.06530.01940.0425-0.05310.0893-0.03180.0279-0.0214-0.0175-0.0924-0.0434-0.078232.72771.833730.4485
41.1168-0.10510.28733.8790.88252.21020.0049-0.21980.11880.2263-0.02430.2341-0.0037-0.08830.0193-0.0153-0.02470.0377-0.0561-0.0821-0.108129.202310.041850.1665
52.5477-0.91640.21092.7087-0.73872.0667-0.06810.18850.2177-0.1059-0.0474-0.10680.0862-0.05070.1155-0.0692-0.0177-0.0207-0.09120.0137-0.023413.57521.4405-6.6341
62.2227-2.06420.26745.1542-3.52633.7792-0.1048-0.1979-0.02070.13530.0285-0.08390.2372-0.08530.07630.28230.0560.007-0.26720.0002-0.265837.6507-14.429254.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|117 }A2 - 117
2X-RAY DIFFRACTION2{ A|133 - A|245 }A133 - 245
3X-RAY DIFFRACTION3{ B|2 - B|117 }B2 - 117
4X-RAY DIFFRACTION4{ B|134 - B|243 }B134 - 243
5X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C299 - 314
6X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C317 - 361
7X-RAY DIFFRACTION5{ C|299 - C|314 C|317 - C|361 C|365 - C|397 }C365 - 397
8X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D300 - 314
9X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D319 - 341
10X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D350 - 359
11X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D365 - 382
12X-RAY DIFFRACTION6{ D|300 - D|314 D|319 - D|341 D|350 - D|359 D|365 - D|382 D|386 - D|393}D386 - 393

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more