[English] 日本語
Yorodumi
- PDB-5bq7: Crystal structure of chikungunya virus-human Fab 5F-10 fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bq7
TitleCrystal structure of chikungunya virus-human Fab 5F-10 fragment
Components
  • Fab 5F-10-Heavy Chain
  • Fab 5F-10-Light Chain
KeywordsIMMUNE SYSTEM / Human antibody Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.738 Å
AuthorsMangala Prasad, V. / Rossmann, M.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI095366 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J Virol / Year: 2016
Title: Structural Studies of Chikungunya Virus-Like Particles Complexed with Human Antibodies: Neutralization and Cell-to-Cell Transmission.
Authors: Jason Porta / Vidya Mangala Prasad / Cheng-I Wang / Wataru Akahata / Lisa F P Ng / Michael G Rossmann /
Abstract: Chikungunya virus is a positive-stranded RNA alphavirus. Structures of chikungunya virus-like particles in complex with strongly neutralizing antibody Fab fragments (8B10 and 5F10) were determined ...Chikungunya virus is a positive-stranded RNA alphavirus. Structures of chikungunya virus-like particles in complex with strongly neutralizing antibody Fab fragments (8B10 and 5F10) were determined using cryo-electron microscopy and X-ray crystallography. By fitting the crystallographically determined structures of these Fab fragments into the cryo-electron density maps, we show that Fab fragments of antibody 8B10 extend radially from the viral surface and block receptor binding on the E2 glycoprotein. In contrast, Fab fragments of antibody 5F10 bind the tip of the E2 B domain and lie tangentially on the viral surface. Fab 5F10 fixes the B domain rigidly to the surface of the virus, blocking exposure of the fusion loop on glycoprotein E1 and therefore preventing the virus from becoming fusogenic. Although Fab 5F10 can neutralize the wild-type virus, it can also bind to a mutant virus without inhibiting fusion or attachment. Although the mutant virus is no longer able to propagate by extracellular budding, it can, however, enter the next cell by traveling through junctional complexes without being intercepted by a neutralizing antibody to the wild-type virus, thus clarifying how cell-to-cell transmission can occur.
IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Chikungunya virus (CHIKV), which belongs to the Alphavirus genus, has a wide distribution in the Old World that has expanded in ...IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Chikungunya virus (CHIKV), which belongs to the Alphavirus genus, has a wide distribution in the Old World that has expanded in recent years into the Americas. There are currently no vaccines or drugs against alphaviral infections. Therefore, a better understanding of CHIKV and its associated neutralizing antibodies will aid in the development of effective treatments.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab 5F-10-Heavy Chain
B: Fab 5F-10-Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5733
Polymers50,4662
Non-polymers1061
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.207, 66.625, 168.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Fab 5F-10-Heavy Chain


Mass: 27691.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293TPM1 / Production host: Homo sapiens (human)
#2: Antibody Fab 5F-10-Light Chain


Mass: 22775.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293TPM1 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% 2-propanol, 25% PEG-4000, 50mM HEPES buffer pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.738→43 Å / Num. all: 11899 / Num. obs: 11899 / % possible obs: 94.42 % / Redundancy: 5 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 7.25
Reflection shellResolution: 2.75→2.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.39 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V0V, 1HZH, 4D9L

3v0v

1hzh

4d9l


Resolution: 2.738→43 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 1182 9.93 %Random selection
Rwork0.2321 ---
obs0.2377 11899 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.738→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 7 28 3165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033216
X-RAY DIFFRACTIONf_angle_d0.8274379
X-RAY DIFFRACTIONf_dihedral_angle_d14.481126
X-RAY DIFFRACTIONf_chiral_restr0.03503
X-RAY DIFFRACTIONf_plane_restr0.004555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7385-2.86310.32231330.28051223X-RAY DIFFRACTION88
2.8631-3.0140.37471440.28931306X-RAY DIFFRACTION95
3.014-3.20280.33071470.29221324X-RAY DIFFRACTION96
3.2028-3.44990.32011420.25021337X-RAY DIFFRACTION96
3.4499-3.79690.33351510.22911340X-RAY DIFFRACTION96
3.7969-4.34590.27111500.21461376X-RAY DIFFRACTION96
4.3459-5.47360.21831530.19111373X-RAY DIFFRACTION96
5.4736-43.0120.27551620.2231438X-RAY DIFFRACTION94
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)
19.4991-1.5091-2.66092.19930.33512.46550.3153-0.424-0.05870.0575-0.3622-0.1964-0.1070.40520.00490.2815-0.0261-0.02760.31420.01530.21497.1388-13.485117.7481
23.81260.6107-0.91165.2089-2.67655.78540.08330.62810.2875-0.4213-0.09980.39870.3442-0.4085-0.04080.28240.0623-0.06790.4718-0.0310.27071.807-17.1116.9137
34.02281.0775-3.47340.8637-1.39464.1069-0.05810.2738-0.0883-0.1294-0.1079-0.06070.0996-0.00660.12720.23660.031-0.05250.2802-0.04380.27-2.9939-18.701421.9328
42.24821.6124-2.13254.3574-0.89635.345-0.0559-0.06940.0047-0.0635-0.0703-0.2162-0.2227-0.04570.050.0880.02030.00260.20460.00350.2049-13.3394-24.992339.8344
54.65980.74621.4438.2004-1.57011.6086-0.2221-0.8658-0.61.3513-0.2511-0.2238-0.35590.76680.5630.4260.09180.09820.5340.1450.3271-14.5896-31.644453.6604
61.50281.9601-0.10867.6938-4.04367.92370.0694-0.30180.62250.29540.01940.1392-0.11560.8973-0.03320.23330.1154-0.06980.3475-0.07720.2889-14.3445-19.079247.561
73.11620.25690.11524.1508-0.66652.5736-0.12690.1734-0.2713-1.00970.42180.27891.1082-0.2054-0.27780.7078-0.0441-0.06240.3589-0.06430.48562.9528-38.385611.6373
82.2324-1.213-0.36242.9185-0.29510.262-0.64440.53030.1142-0.64660.1679-0.99760.54840.0730.19060.9801-0.08380.2240.6083-0.00350.63428.921-39.421711.6152
93.44850.5776-1.18751.87620.3482.8519-0.0328-0.0966-0.1382-0.2678-0.05930.07030.1743-0.18610.03310.25760.0049-0.02750.20320.05340.2676-22.2181-35.160933.7477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 182 )
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 199 )
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 221 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 50 )
8X-RAY DIFFRACTION8chain 'B' and (resid 51 through 100 )
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 216 )

+
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://pdbjlvh1.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