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- PDB-7jph: Crystal structure of EBOV glycoprotein with modified HR1c and HR2... -

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Basic information

Entry
Database: PDB / ID: 7jph
TitleCrystal structure of EBOV glycoprotein with modified HR1c and HR2 stalk at 3.2 A resolution
Components(Envelope glycoprotein) x 2
KeywordsVIRAL PROTEIN / Ebola glycoprotein
Function / homology
Function and homology information


symbiont-mediated killing of host cell / 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 / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / 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 / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / 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
PHOSPHATE ION / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.195 Å
AuthorsChaudhary, A. / Stanfield, R.L. / Wilson, I.A. / Zhu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129698 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140844 United States
CitationJournal: Nat Commun / Year: 2021
Title: Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines.
Authors: He, L. / Chaudhary, A. / Lin, X. / Sou, C. / Alkutkar, T. / Kumar, S. / Ngo, T. / Kosviner, E. / Ozorowski, G. / Stanfield, R.L. / Ward, A.B. / Wilson, I.A. / Zhu, J.
History
DepositionAug 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0947
Polymers51,0602
Non-polymers2,0355
Water00
1
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,28321
Polymers153,1796
Non-polymers6,10415
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area39460 Å2
ΔGint-102 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.061, 114.061, 136.216
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein


Mass: 31591.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human)
#2: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 19467.996 Da / Num. of mol.: 1 / Mutation: T577P,W615L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q05320

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Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 2
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

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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Details

Has ligand of interestN
Has protein modificationY
Sequence detailsThe complete sequence of chain A is IPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSG ...The complete sequence of chain A is IPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSG VPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGD FAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDP SSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSN TTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSTHHQDTGEESASSGK LGLITNTIAGVAGLITGGRRTRR

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium citrate, 10% PEG w/v 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.195→49.439 Å / Num. obs: 17343 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.776 / Net I/σ(I): 8.4
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 0.45 / Num. unique obs: 864 / CC1/2: 0.313 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ3

5jq3


Resolution: 3.195→49.439 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.84 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.214 / SU B: 35.246 / SU ML: 0.507 / Average fsc free: 0.7129 / Average fsc work: 0.7231 / Cross valid method: FREE R-VALUE / ESU R: 0.911 / ESU R Free: 0.471
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3216 837 4.9 %
Rwork0.2766 16245 -
all0.279 --
obs-17082 97.65 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 93.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.131 Å2-0.565 Å2-0 Å2
2---1.131 Å20 Å2
3---3.668 Å2
Refinement stepCycle: LAST / Resolution: 3.195→49.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 91 0 3256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133344
X-RAY DIFFRACTIONr_bond_other_d0.0130.0172981
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1240.014063
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.7054564
X-RAY DIFFRACTIONr_angle_other_deg1.5891.6246939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7535392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87122.619168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69915507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3461518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02702
X-RAY DIFFRACTIONr_nbd_refined0.2160.2634
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.22882
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21581
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.210
X-RAY DIFFRACTIONr_nbd_other0.2030.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.22
X-RAY DIFFRACTIONr_mcbond_it7.7779.9141586
X-RAY DIFFRACTIONr_mcbond_other7.7669.9041585
X-RAY DIFFRACTIONr_mcangle_it12.40814.8361972
X-RAY DIFFRACTIONr_mcangle_other12.40714.8471973
X-RAY DIFFRACTIONr_scbond_it7.84910.4891758
X-RAY DIFFRACTIONr_scbond_other7.84910.4891758
X-RAY DIFFRACTIONr_scangle_it12.70215.5792592
X-RAY DIFFRACTIONr_scangle_other12.715.582593
X-RAY DIFFRACTIONr_lrange_it16.706176.8376238
X-RAY DIFFRACTIONr_lrange_other16.704176.8386239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.195-3.2780.371770.361084X-RAY DIFFRACTION90.774
3.278-3.3680.346460.3611188X-RAY DIFFRACTION99.6769
3.368-3.4660.498530.5061139X-RAY DIFFRACTION99.1681
3.466-3.5720.297610.3931099X-RAY DIFFRACTION98.8075
3.572-3.6890.589480.521093X-RAY DIFFRACTION99.7378
3.689-3.8190.371460.3871038X-RAY DIFFRACTION98.9051
3.819-3.9630.531400.512900X-RAY DIFFRACTION89.0152
3.963-4.1240.369370.358907X-RAY DIFFRACTION91.4729
4.124-4.3080.339420.227910X-RAY DIFFRACTION97.7413
4.308-4.5180.246760.168870X-RAY DIFFRACTION99.5789
4.518-4.7620.244360.152865X-RAY DIFFRACTION99.7785
4.762-5.050.171320.17817X-RAY DIFFRACTION100
5.05-5.3980.257470.171766X-RAY DIFFRACTION100
5.398-5.830.228460.183703X-RAY DIFFRACTION100
5.83-6.3850.286490.191647X-RAY DIFFRACTION100
6.385-7.1370.291320.196609X-RAY DIFFRACTION99.226
7.137-8.2370.297170.192547X-RAY DIFFRACTION100
8.237-10.0790.2220.177466X-RAY DIFFRACTION100
10.079-14.2150.265220.188374X-RAY DIFFRACTION99.7481
14.215-49.4390.4680.38223X-RAY DIFFRACTION95.8506

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