[English] 日本語
Yorodumi
- PDB-7lsg: Crystal structure of the human neutralizing antibody Fab fragment... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lsg
TitleCrystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Siberian Subtype)
Components
  • Core proteinCapsid
  • T025 Fab Heavy Chain
  • T025 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Tick-borne encephalitis virus / antibody / EDIII / TBEV / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. ...Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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 / 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Tick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Exp.Med. / Year: 2021
Title: Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease.
Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / ...Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / Teislerova, D. / Chrdle, A. / Honig, V. / Oliveira, T. / West, A.P. / Lee, Y.E. / Rice, C.M. / MacDonald, M.R. / Bjorkman, P.J. / Ruzek, D. / Robbiani, D.F. / Nussenzweig, M.C.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
H: T025 Fab Heavy Chain
L: T025 Fab Light Chain
C: Core protein


Theoretical massNumber of molelcules
Total (without water)58,9383
Polymers58,9383
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area23790 Å2
Unit cell
Length a, b, c (Å)55.439, 67.230, 91.160
Angle α, β, γ (deg.)90.000, 94.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody T025 Fab Heavy Chain


Mass: 24834.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody T025 Fab Light Chain


Mass: 23424.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 10678.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Strain: Vasilchenko / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G8FGD9, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% (+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES pH 7.5, 10% PEG 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.86→90.84 Å / Num. obs: 53401 / % possible obs: 95.8 % / Redundancy: 6 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Net I/σ(I): 8.5 / Num. measured all: 320468 / Scaling rejects: 533
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.9161.0912106235280.7220.4831.1971.698.1
8.94-90.846.20.07932455260.9940.0330.08618.594.9

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGX, 6J5F

4ogx

6j5f


Resolution: 1.86→49.06 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 2530 4.74 %
Rwork0.1867 50823 -
obs0.188 53353 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.93 Å2
Refinement stepCycle: LAST / Resolution: 1.86→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 0 325 4301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01724081
X-RAY DIFFRACTIONf_angle_d1.43565562
X-RAY DIFFRACTIONf_chiral_restr0.0895622
X-RAY DIFFRACTIONf_plane_restr0.0098718
X-RAY DIFFRACTIONf_dihedral_angle_d16.49961460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.30111510.2812859X-RAY DIFFRACTION97.89
1.9-1.940.2821300.27782889X-RAY DIFFRACTION97.23
1.94-1.980.27351430.24582865X-RAY DIFFRACTION96.6
1.98-2.030.26531270.23132810X-RAY DIFFRACTION95.89
2.03-2.080.26951390.22232718X-RAY DIFFRACTION93.06
2.08-2.130.24091350.21012615X-RAY DIFFRACTION89.17
2.13-2.20.22651460.20482883X-RAY DIFFRACTION97.87
2.2-2.270.2371430.20692873X-RAY DIFFRACTION97.76
2.27-2.350.25291430.20572873X-RAY DIFFRACTION97.07
2.35-2.440.251060.20312831X-RAY DIFFRACTION95.7
2.44-2.550.24731260.20842710X-RAY DIFFRACTION91.16
2.55-2.690.22841410.19762802X-RAY DIFFRACTION94.87
2.69-2.860.20691450.19812904X-RAY DIFFRACTION98.48
2.86-3.080.21951510.1922882X-RAY DIFFRACTION96.99
3.08-3.390.21031490.17932687X-RAY DIFFRACTION91.28
3.39-3.880.18331470.15862896X-RAY DIFFRACTION98.13
3.88-4.880.1561420.1452818X-RAY DIFFRACTION94.12
4.88-49.060.21481660.18242908X-RAY DIFFRACTION95.53

+
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