[English] 日本語
Yorodumi
- PDB-4bz2: Structure of dengue virus EDIII in complex with Fab 2D73 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bz2
TitleStructure of dengue virus EDIII in complex with Fab 2D73
Components
  • ENVELOPE PROTEINViral envelope
  • FAB 2D73 HEAVY CHAIN
  • FAB 2D73 LIGHT CHAIN
KeywordsIMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / IMMUNE SYSTEM / ANTIBODY / IMMUNOGLOBULIN / FUSION LOOP / VIRION
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / 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 / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 4
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsLi, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. ...Li, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. / Che, X.Y. / Young, P.R. / Kobe, B.
CitationJournal: To be Published
Title: Structure of Dengue Virus Ediii in Complex with Fab 2D73
Authors: Li, J. / Watterson, D. / Chang, C.W. / Li, X.Q. / Ericsson, D.J. / Qiu, L.W. / Cai, J.P. / Chen, J. / Fry, S.R. / Cooper, M.A. / Che, X.Y. / Young, P.R. / Kobe, B.
History
DepositionJul 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENVELOPE PROTEIN
H: FAB 2D73 HEAVY CHAIN
L: FAB 2D73 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,53418
Polymers58,8613
Non-polymers67315
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-27.3 kcal/mol
Surface area29280 Å2
MethodPQS
Unit cell
Length a, b, c (Å)108.655, 108.655, 108.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ENVELOPE PROTEIN / Viral envelope


Mass: 11284.909 Da / Num. of mol.: 1 / Fragment: DOMAIN 3, RESIDUES 301-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 4 / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: Q7TGC7

-
Antibody , 2 types, 2 molecules HL

#2: Antibody FAB 2D73 HEAVY CHAIN


Mass: 24015.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C
#3: Antibody FAB 2D73 LIGHT CHAIN


Mass: 23560.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C

-
Non-polymers , 5 types, 118 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM ACETATE PH 5.0, 23% (W/V) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953693
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 2.03→48.59 Å / Num. obs: 42571 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.59
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 2.03 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R29

2r29


Resolution: 2.03→48.592 Å / SU ML: 0.25 / σ(F): 1.85 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2148 5.1 %
Rwork0.2052 --
obs0.2062 42567 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.7 Å2
Refinement stepCycle: LAST / Resolution: 2.03→48.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 36 103 4223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154236
X-RAY DIFFRACTIONf_angle_d0.75727
X-RAY DIFFRACTIONf_dihedral_angle_d11.8611530
X-RAY DIFFRACTIONf_chiral_restr0.044632
X-RAY DIFFRACTIONf_plane_restr0.002723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.07720.33161470.30422651X-RAY DIFFRACTION100
2.0772-2.12920.30011440.27732657X-RAY DIFFRACTION100
2.1292-2.18670.27561380.24342647X-RAY DIFFRACTION100
2.1867-2.25110.2711520.24712648X-RAY DIFFRACTION100
2.2511-2.32370.29051350.23382654X-RAY DIFFRACTION100
2.3237-2.40680.23271390.22122658X-RAY DIFFRACTION100
2.4068-2.50320.24161490.21842643X-RAY DIFFRACTION100
2.5032-2.61710.24921160.22352687X-RAY DIFFRACTION100
2.6171-2.7550.28931310.23062697X-RAY DIFFRACTION100
2.755-2.92760.26721520.22782696X-RAY DIFFRACTION100
2.9276-3.15360.26011380.22432690X-RAY DIFFRACTION100
3.1536-3.47090.22381550.20772696X-RAY DIFFRACTION100
3.4709-3.9730.20531480.18912718X-RAY DIFFRACTION100
3.973-5.00470.18751650.1612745X-RAY DIFFRACTION100
5.0047-48.60590.19671390.20322932X-RAY DIFFRACTION100
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)
17.8174-2.20520.55554.3669-0.87343.56450.0691-0.7166-0.62910.1933-0.1458-0.15890.59820.55180.03490.36190.03120.01640.40470.08510.273818.937621.615-12.7626
25.5075-1.29710.35478.6017-0.92560.66120.168-1.1134-0.08981.4757-0.4311-0.03460.0711.50220.27720.7891-0.03210.02881.91490.20730.560254.219724.5795-9.5896
33.80412.0825-0.42523.5984-0.42532.88910.1362-0.14870.4330.1009-0.03010.0057-0.15780.3363-0.08030.24870.01910.06340.3268-0.01260.291522.58838.6436-25.1449
43.8976-1.3422-0.30620.8817-0.99151.8206-0.1195-0.8771-0.18570.0277-0.0178-0.35220.37241.14430.15220.45870.1178-0.07231.20110.06730.645655.35528.1573-25.0634
52.0237-0.0225-0.29375.472-0.81231.982-0.0501-0.8902-0.3795-0.3821-0.1271-0.40350.44060.75020.17320.46750.0819-0.06261.17370.16050.66958.040525.5073-26.1466
62.20785.27768.81255.64155.02067.77670.17970.9715-0.1037-0.390.19780.1637-0.3081.0784-0.34920.3991-0.0410.07740.51820.01120.3468-7.47617.7462-36.0457
74.43531.80741.3664.28443.29837.42580.07730.13830.03750.07460.04680.14390.2253-0.2608-0.13080.2052-0.04140.03950.23110.02310.2496-1.125826.1695-27.088
89.81298.0417-7.17542.0762-8.96819.9745-0.33360.66540.6142-0.30420.64050.55760.2751-0.4053-0.39920.3762-0.0469-0.01240.3056-0.04130.4283-13.58822.5181-16.7981
97.1312-6.1819-4.52156.7346.347.8970.0189-0.0613-0.0565-0.90490.48230.0934-0.25890.3718-0.43170.4874-0.13880.08420.37080.00720.4258-4.522825.1492-34.7777
106.0199-0.9253-1.16140.5012-1.25917.64640.2347-0.10730.1581-0.01970.20990.01930.0806-0.1824-0.40820.1972-0.04140.02970.2259-0.00420.3343-5.517825.9428-18.1657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H AND (RESID 1 THROUGH 127 )
2X-RAY DIFFRACTION2CHAIN H AND (RESID 128 THROUGH 221 )
3X-RAY DIFFRACTION3CHAIN L AND (RESID 1 THROUGH 101 )
4X-RAY DIFFRACTION4CHAIN L AND (RESID 102 THROUGH 155 )
5X-RAY DIFFRACTION5CHAIN L AND (RESID 156 THROUGH 212 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 296 THROUGH 308 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 309 THROUGH 336 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 337 THROUGH 350 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 351 THROUGH 363 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 364 THROUGH 396 )

+
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