[English] 日本語
Yorodumi
- PDB-6flb: 3H5 Fab bound to EDIII of DenV 2 Xtal form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6flb
Title3H5 Fab bound to EDIII of DenV 2 Xtal form 2
Components
  • Domain III of Dengue virus 2
  • Heavy chain of 3H5 Fab
  • Light chain of 3H5 Fab
KeywordsVIRAL PROTEIN / Dengue virus / antibody / macromolecular complex
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / viral capsid / 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / : / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFlanagan, A. / Renner, M. / Grimes, J.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204703/Z/16/Z United Kingdom
Wellcome Trust075491/Z/04 United Kingdom
CitationJournal: Nat. Immunol. / Year: 2018
Title: Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus.
Authors: Renner, M. / Flanagan, A. / Dejnirattisai, W. / Puttikhunt, C. / Kasinrerk, W. / Supasa, P. / Wongwiwat, W. / Chawansuntati, K. / Duangchinda, T. / Cowper, A. / Midgley, C.M. / Malasit, P. / ...Authors: Renner, M. / Flanagan, A. / Dejnirattisai, W. / Puttikhunt, C. / Kasinrerk, W. / Supasa, P. / Wongwiwat, W. / Chawansuntati, K. / Duangchinda, T. / Cowper, A. / Midgley, C.M. / Malasit, P. / Huiskonen, J.T. / Mongkolsapaya, J. / Screaton, G.R. / Grimes, J.M.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Domain III of Dengue virus 2
H: Heavy chain of 3H5 Fab
L: Light chain of 3H5 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0398
Polymers59,6333
Non-polymers4075
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-57 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.492, 131.573, 139.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules G

#1: Protein Domain III of Dengue virus 2


Mass: 11163.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14340, UniProt: W5RZ25*PLUS

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of 3H5 Fab


Mass: 24438.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Light chain of 3H5 Fab


Mass: 24030.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 425 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.2 M Ammonium di Hydrogen Phosphate using a protein concentration of 6 mg/ml.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→21.3 Å / Num. obs: 37183 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.52 Å2 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.3 Å

-
Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→21.29 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9381 / SU R Cruickshank DPI: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1860 5 %RANDOM
Rwork0.1755 ---
obs0.1776 37183 99.21 %-
Displacement parametersBiso mean: 44.18 Å2
Baniso -1Baniso -2Baniso -3
1-4.0302 Å20 Å20 Å2
2---0.6429 Å20 Å2
3----3.3872 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: 1 / Resolution: 2.2→21.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 24 420 4500
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014177HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1391SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes600HARMONIC5
X-RAY DIFFRACTIONt_it4177HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion17.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion557SEMIHARMONIC5
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_contact4837SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2569 113 4.33 %
Rwork0.2035 2498 -
all0.2059 2611 -
obs--99.21 %
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)
11.64150.51430.29336.1872-1.57012.3246-0.16940.2318-0.0301-0.4357-0.0031-0.2123-0.00210.05290.17250.0036-0.13130.059-0.0237-0.0566-0.14731.3583-42.7875-32.9928
21.39870.7537-0.20585.1543-1.93310.2752-0.16680.3118-0.0214-0.2661-0.0744-0.0242-0.07220.08520.24120.059-0.10650.01740.0054-0.0503-0.13133.09-38.9121-33.023
31.97930.69791.31032.24491.00143.3817-0.0148-0.08420.00510.24050.036-0.30960.03160.054-0.0212-0.0083-0.016-0.0864-0.06820.0367-0.007218.4903-14.1048-25.4835
41.16481.08190.60070.008-0.56160.4476-0.0023-0.00710.03320.0092-0.0481-0.11950.01380.12140.0503-0.04220.0013-0.0243-0.0848-0.02150.139124.5602-13.4834-30.977
51.65051.1895-0.11773.13890.15971.6865-0.00940.0264-0.02190.5442-0.04030.0254-0.53570.010.04970.1937-0.06880.0044-0.0779-0.0233-0.13740.6024-42.0018-10.5437
60.03340.23980.52140.29510.05810.56070.0005-0.0205-0.01280.0480.01680.0327-0.05360.0003-0.01730.2616-0.03340.0904-0.0418-0.0233-0.203-5.743-46.3471-5.3463
70.29430.39060.09922.185-0.071500.0666-0.01410.04550.5314-0.148-0.0893-0.1701-0.08660.08130.163-0.0897-0.0529-0.0969-0.0025-0.16737.4188-21.9204-14.4675
80.9807-0.06620.39013.5843-0.11871.06920.0799-0.14160.24950.1347-0.10540.0635-0.2245-0.36560.02560.2228-0.0254-0.0725-0.1183-0.0017-0.15129.5353-3.6716-16.9286
90.78131.12540.21221.30420.48060.2925-0.0121-0.03550.0133-0.01080.0134-0.02680.00390.001-0.0014-0.0378-0.01780.0678-0.005-0.07260.08151.0545-63.0021-20.878
100-0.3884-1.60581.34471.69810.04980.0063-0.022-0.0232-0.03880.01220.0124-0.0055-0.0433-0.0185-0.0343-0.0439-0.0149-0.0441-0.03460.0811-13.5177-74.812-28.681
110.2873-2.42131.64583.17950.36231.27120.0104-0.0149-0.0411-0.0790.023-0.0033-0.0180.0271-0.0333-0.0611-0.00660.04840.0053-0.05350.0416-5.3289-70.5137-25.1561
120.10860.2886-0.39211.1069-0.59381.8640.0008-0.011-0.0127-0.03780.0103-0.0353-0.03670.0141-0.0112-0.1096-0.00010.0086-0.0166-0.06140.0813-10.3199-63.0081-18.3649
130.74291.6828-0.66161.1895-0.15110.06660.0051-0.0781-0.02730.0417-0.0494-0.0367-0.1157-0.03110.0442-0.13720.02410.01740.0885-0.02370.0551-13.7764-66.2284-14.6166
140.6965-0.27990.506401.04990.31140.00010.0163-0.0094-0.04950.0007-0.00750.00480.0059-0.0008-0.1353-0.04780.05710.0411-0.07980.10343.1236-71.1809-24.8847
150.27341.2449-0.14591.46470.74551.8592-0.0084-0.0635-0.1208-0.08310.05710.0816-0.1168-0.1221-0.0487-0.1025-0.0069-0.00720.018-0.01710.0699-14.2096-66.1021-21.3789
160.46970.372-0.44050.03252.24251.37770.0046-0.0146-0.1104-0.110.01250.1441-0.2124-0.0394-0.0171-0.14840.0315-0.03560.0567-0.00820.1118-19.6452-67.0187-24.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ H|1 - H|71 }
2X-RAY DIFFRACTION2{ H|72 - H|119 }
3X-RAY DIFFRACTION3{ H|120 - H|194 }
4X-RAY DIFFRACTION4{ H|195 - H|218 }
5X-RAY DIFFRACTION5{ L|1 - L|67 }
6X-RAY DIFFRACTION6{ L|68 - L|77 }
7X-RAY DIFFRACTION7{ L|78 - L|151 }
8X-RAY DIFFRACTION8{ L|152 - L|216 }
9X-RAY DIFFRACTION9{ G|298 - G|307 }
10X-RAY DIFFRACTION10{ G|308 - G|316 }
11X-RAY DIFFRACTION11{ G|317 - G|331 }
12X-RAY DIFFRACTION12{ G|332 - G|343 }
13X-RAY DIFFRACTION13{ G|344 - G|355 }
14X-RAY DIFFRACTION14{ G|356 - G|365 }
15X-RAY DIFFRACTION15{ G|366 - G|384 }
16X-RAY DIFFRACTION16{ G|385 - G|397 }

+
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