[English] 日本語
Yorodumi
- PDB-7lyd: Crystal Structure of Ebola zaire Envelope glycoprotein GP in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lyd
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146
Components
  • GP1
  • GP2
KeywordsVIRAL PROTEIN / SSGCID / Envelope glycoprotein / Zaire ebolavirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Chem-YOD / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
A: GP1
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,62410
Polymers51,2322
Non-polymers2,3928
Water3,243180
1
A: GP1
B: GP2
hetero molecules

A: GP1
B: GP2
hetero molecules

A: GP1
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,87230
Polymers153,6956
Non-polymers7,17724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area36450 Å2
ΔGint-81 kcal/mol
Surface area49250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.170, 114.170, 308.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein GP1


Mass: 32309.303 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed N-terminal domain / Mutation: T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320
#2: Protein GP2


Mass: 18922.320 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed C-terminal domain / Mutation: H613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320

-
Sugars , 2 types, 5 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 183 molecules

#5: Chemical ChemComp-YOD / (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide


Mass: 412.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36N2OS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY
Sequence detailsResidues in the C-terminal portion of chain A were difficult to identify, and so were modeled as ...Residues in the C-terminal portion of chain A were difficult to identify, and so were modeled as UNK. The actual sequence for chain A is: ETGRSIPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a. ...Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml: over night soak with 1mM compound ARN0075146 (BSI110990): tray 313149a11, cryo: direct: puck hdp6-5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 14, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 32679 / % possible obs: 99.9 % / Redundancy: 6.824 % / Biso Wilson estimate: 54.11 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.26
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2366 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6F5U

6f5u


Resolution: 2.35→41.63 Å / SU ML: 0.267 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.961
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2032 6.23 %0
Rwork0.177 ---
obs0.179 32635 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 158 180 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063014
X-RAY DIFFRACTIONf_angle_d0.7364119
X-RAY DIFFRACTIONf_dihedral_angle_d12.31054
X-RAY DIFFRACTIONf_chiral_restr0.048487
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.29731320.26112003X-RAY DIFFRACTION100
2.4-2.460.29191170.23972012X-RAY DIFFRACTION99
2.46-2.530.27991360.22012026X-RAY DIFFRACTION100
2.53-2.610.24071340.20242014X-RAY DIFFRACTION100
2.61-2.690.21831380.19241999X-RAY DIFFRACTION100
2.69-2.790.24391480.19952038X-RAY DIFFRACTION100
2.79-2.90.28221260.19662009X-RAY DIFFRACTION100
2.9-3.030.19691570.1812005X-RAY DIFFRACTION100
3.03-3.190.21961310.17782027X-RAY DIFFRACTION100
3.19-3.390.21071220.18762063X-RAY DIFFRACTION100
3.39-3.650.19611490.17262012X-RAY DIFFRACTION100
3.65-4.020.18241420.15432054X-RAY DIFFRACTION100
4.02-4.60.15281230.13372082X-RAY DIFFRACTION100
4.6-5.790.19121510.16162080X-RAY DIFFRACTION100
5.79-41.630.211260.19882179X-RAY DIFFRACTION99
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)
16.5394-2.26231.37567.3042-1.95046.6346-0.6342-2.0747-1.30671.49121.0730.48380.5944-1.3515-0.39310.77330.00530.13640.66920.09080.4025-57.152511.62760.6838
29.31613.7452-4.84578.98991.01997.2091-0.6924-0.3565-1.45971.29750.1526-0.12771.6102-0.94680.49661.10550.05770.1370.84670.10020.6782-57.931319.90046.3543
31.9228-0.620.00021.95870.64483.8394-0.01220.152-0.1599-0.1974-0.11510.01950.4215-0.07080.11920.3903-0.01980.040.25160.01590.3115-55.234612.6382-26.5834
41.1823-0.53-0.89755.24613.64038.1665-0.15890.1667-0.1047-0.4372-0.0962-0.0650.60930.46920.22860.47870.06860.08430.28410.07870.3926-51.28615.9604-29.8044
55.15940.8607-0.77967.51271.41898.7874-0.43170.1474-0.6965-0.182-0.0177-0.17381.38970.38860.47711.040.14090.17950.4339-0.030.5234-44.5141-5.5689-39.1015
60.80591.1431.17264.97433.72933.0735-0.18190.214-0.1861-0.19130.026-0.291.76370.6160.15171.05650.2570.12190.56640.00420.6471-46.1945-7.249-38.3563
76.53432.95790.40795.5354-0.93864.5541-0.0498-0.118-0.48050.6027-0.0371-0.06320.93940.0580.08660.72460.04190.07290.32660.04150.4049-50.53734.0045-10.3394
87.22345.79941.93374.66981.27682.33722.0761-2.4069-0.10461.9429-1.90140.20680.49741.033-0.11080.7282-0.18060.02430.88480.12131.1827-33.93826.4546-12.7556
91.65442.6508-1.13984.9702-1.29191.0162-0.130.008-0.2184-0.0378-0.0337-0.68520.18150.08340.18280.39220.1130.01490.54370.06830.525-36.416120.4039-17.7303
102.7775-1.02680.22953.8524-0.92863.2248-0.1448-0.1929-0.08780.24390.03590.11720.3167-0.29030.0850.3964-0.05540.04480.3491-0.01620.3719-59.573314.9485-12.095
117.5914-0.99150.0875.2804-0.43896.4319-0.0967-1.3902-0.3991.4772-0.12630.74120.4727-1.16490.15230.7436-0.05560.07410.63780.04610.4518-60.495827.22798.1739
120.05270.0635-0.07740.0648-0.07690.10080.0627-0.17360.40840.8355-0.7045-0.31241.67910.16690.57381.6633-0.2188-0.243.3846-0.34520.9844-50.128530.45635.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 31 THROUGH 45 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 46 THROUGH 59 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 60 THROUGH 176 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 177 THROUGH 237 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 238 THROUGH 263 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 264 THROUGH 293 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 502 THROUGH 519 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 520 THROUGH 529 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 530 THROUGH 550 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 551 THROUGH 583 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 584 THROUGH 612 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 613 THROUGH 629 )

+
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