[English] 日本語
Yorodumi
- PDB-6tou: Rabies virus glycoprotein PH domain in complex with the scFv frag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tou
TitleRabies virus glycoprotein PH domain in complex with the scFv fragment of broadly neutralizing human antibody RVC20
Components
  • Glycoprotein,Glycoprotein
  • Single-chain Fv
KeywordsVIRAL PROTEIN / glycoprotein / antibody
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain / viral envelope / virion membrane / membrane / Glycoprotein
Function and homology information
Biological speciesRabies lyssavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsHellert, J. / Rey, F.A.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the prefusion-locking broadly neutralizing antibody RVC20 bound to the rabies virus glycoprotein.
Authors: Hellert, J. / Buchrieser, J. / Larrous, F. / Minola, A. / de Melo, G.D. / Soriaga, L. / England, P. / Haouz, A. / Telenti, A. / Schwartz, O. / Corti, D. / Bourhy, H. / Rey, F.A.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Glycoprotein,Glycoprotein
A: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7686
Polymers40,6212
Non-polymers1464
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-42 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.945, 81.945, 155.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1333-

HOH

-
Components

#1: Protein Glycoprotein,Glycoprotein


Mass: 13100.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies lyssavirus / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JUA9
#2: Antibody Single-chain Fv


Mass: 27520.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.7 uL of 18 mg/mL complex in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.7 uL of reservoir solution containing 100 mM Tris-Cl pH 8.0, 300 mM CaCl2, 22% w/v PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 1, 2019
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.587→46.506 Å / Num. obs: 15457 / % possible obs: 89.5 % / Redundancy: 25.7 % / Biso Wilson estimate: 84.61 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.106 / Rsym value: 0.103 / Net I/σ(I): 21.374
Reflection shellResolution: 2.587→2.72 Å / Redundancy: 28.1 % / Num. unique obs: 774 / CC1/2: 0.66 / Rpim(I) all: 0.705 / Rrim(I) all: 3.758 / Rsym value: 3.69 / % possible all: 33.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 homology model of RVC20 scFv

Resolution: 2.587→46.506 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.225 1545 10 %
Rwork0.1898 --
obs0.1932 15454 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 294.92 Å2 / Biso mean: 105.8974 Å2 / Biso min: 58.68 Å2
Refinement stepCycle: final / Resolution: 2.587→46.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 818 88 3229
Biso mean--84.94 93.35 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032382
X-RAY DIFFRACTIONf_angle_d0.6073228
X-RAY DIFFRACTIONf_chiral_restr0.042351
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d13.4551394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5873-2.67080.4197250.351722716
2.6708-2.76620.35081120.3394100073
2.7662-2.8770.34111410.2836127192
2.877-3.00790.35461550.28941394100
3.0079-3.16640.29311530.24371385100
3.1664-3.36480.23591540.2261385100
3.3648-3.62450.24231570.20451409100
3.6245-3.9890.20081580.17181421100
3.989-4.56580.17141580.14391421100
4.5658-5.75080.20461600.14891445100
5.7508-46.5060.231720.20441551100
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)
19.82752.5219-4.23972.59470.60232.974-0.2809-1.615-0.61540.66861.02230.52651.30950.326-0.72061.08470.10040.07881.76450.621.4128-1.0224-35.8708-8.9941
28.5887-5.7089-5.68723.87393.22519.87140.9469-3.6277-2.37141.9986-1.47441.40012.054-3.57470.72871.9564-0.6887-0.08213.20520.87671.4793.6689-33.32165.4038
33.1777-1.6814-3.41336.67023.59414.23391.0868-1.6726-0.5960.9473-0.1721-2.31031.1199-1.6044-1.09280.796-0.2004-0.33471.39190.51031.202512.9883-30.6188-6.3226
47.27991.5384.75937.6612-1.84894.18050.1822-1.9735-1.68690.0860.4606-0.26480.3141-0.0742-0.72350.7296-0.12950.10121.27490.47620.94688.734-31.2521-10.8023
56.4591-6.10925.97785.737-5.68835.5683-0.2967-3.2525-0.89131.8625-0.2319-0.6892-0.17060.79470.21040.9277-0.06880.00652.37540.65141.39459.1614-33.1294-3.7477
66.1167-5.19664.4534.4034-3.76913.2437-0.1177-1.08381.08682.08171.5084-0.0586-2.53523.9441-1.06952.3229-0.1713-0.77431.98360.31391.755516.3182-21.9648-4.2545
74.0663-4.0480.13454.1658-0.76572.2611-1.0823-0.2855-0.06180.4722-0.1332-1.16953.61050.08021.16141.60050.08340.18731.57660.24190.998519.4508-32.346-10.4728
86.9351-5.8089-4.68994.90693.72353.33461.51072.2925-0.2874-1.4671-1.94090.6371-0.3251-1.5271-0.08151.1092-0.0284-0.06951.30840.01020.826-15.9382-27.882-31.0558
95.5048-1.797-3.4232.70310.36251.94120.27340.01820.3573-0.2398-0.33561.7208-0.23-0.86470.28770.6066-0.0389-0.08470.93810.14761.0165-20.7039-18.6392-18.4711
106.0153-1.5176-5.87622.24321.1595.8304-0.08051.923-1.454-0.182-0.52470.465-0.25580.52141.1541.1639-0.0360.02591.02680.07291.1061-10.0786-38.2594-25.7338
118.3852-1.9476-0.48737.5138-0.29114.6020.0087-0.898-0.56160.41360.1148-0.02060.2766-0.1911-0.11380.4833-0.0852-0.05190.93670.18180.6044-10.4948-24.9186-17.3262
127.2652-4.361-3.27746.70.22944.50530.3329-0.53510.4167-0.2418-0.2211-0.83510.30330.4183-0.110.5034-0.1941-0.07580.7610.07130.6936-5.6649-24.4943-22.5959
135.5227-2.0287-5.23623.31740.76555.23690.67090.76970.6822-0.37690.3019-0.5547-0.1923-1.7216-0.88220.6869-0.0834-0.04061.00370.24520.9136-17.8734-12.5194-23.3091
148.231-2.89926.54297.0301-3.7947.99960.0072-0.2687-0.0014-0.13850.53480.0801-0.9026-0.993-0.64210.4987-0.04910.05070.6065-0.01170.61425.183-11.2669-34.5162
158.06540.04820.31467.3648-1.21827.64610.2276-0.1261-0.7044-0.47490.1585-0.0290.38440.0992-0.42850.4762-0.00210.00750.60810.04260.48434.7832-21.3998-34.7837
163.80410.7236-2.1474.9908-0.873.9287-0.03350.1885-0.1234-0.26190.09410.1229-0.2622-0.5467-0.13950.5078-0.04490.01690.76610.03270.62560.5678-16.2831-34.7091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 41 through 196 )G41 - 196
2X-RAY DIFFRACTION2chain 'G' and (resid 197 through 218 )G197 - 218
3X-RAY DIFFRACTION3chain 'G' and (resid 219 through 227 )G219 - 227
4X-RAY DIFFRACTION4chain 'G' and (resid 228 through 234 )G228 - 234
5X-RAY DIFFRACTION5chain 'G' and (resid 235 through 244 )G235 - 244
6X-RAY DIFFRACTION6chain 'G' and (resid 245 through 249 )G245 - 249
7X-RAY DIFFRACTION7chain 'G' and (resid 250 through 255 )G250 - 255
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 7 )A1 - 7
9X-RAY DIFFRACTION9chain 'A' and (resid 8 through 25 )A8 - 25
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 34 )A26 - 34
11X-RAY DIFFRACTION11chain 'A' and (resid 35 through 82 )A35 - 82
12X-RAY DIFFRACTION12chain 'A' and (resid 82A through 103 )A82A - 103
13X-RAY DIFFRACTION13chain 'A' and (resid 104 through 113 )A104 - 113
14X-RAY DIFFRACTION14chain 'A' and (resid 1000 through 1018 )A1000 - 1018
15X-RAY DIFFRACTION15chain 'A' and (resid 1019 through 1075 )A1019 - 1075
16X-RAY DIFFRACTION16chain 'A' and (resid 1076 through 1107 )A1076 - 1107

+
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