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- PDB-6epk: CRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROT... -

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Basic information

Entry
Database: PDB / ID: 6epk
TitleCRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROTEIN HETERODIMER FROM THE YELLOW FEVER VIRUS
Components
  • Envelope protein E
  • Precursor Membrane Protein
KeywordsVIRAL PROTEIN / PRM-E PROTEIN COMPLEX / HETERODIMER / MATURATION
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / 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, flavivirus / Flavivirus envelope glycoprotein M / 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 / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesYellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRey, F.A. / Duquerroy, S. / Crampon, E. / Barba-Spaeth, G.
CitationJournal: Mbio / Year: 2023
Title: New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex
Authors: Crampon, E. / Covernton, E. / Vaney, M.C. / Dellarole, M. / Sommer, S. / Sharma, A. / Haouz, A. / England, P. / Lepault, J. / Duquerroy, S. / Rey, F.A. / Barba-Spaeth, G.
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein E
B: Precursor Membrane Protein
D: Envelope protein E
E: Precursor Membrane Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,56844
Polymers113,0374
Non-polymers6,53240
Water3,693205
1
A: Envelope protein E
B: Precursor Membrane Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,70122
Polymers56,5182
Non-polymers3,18320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Envelope protein E
E: Precursor Membrane Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86722
Polymers56,5182
Non-polymers3,34920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.880, 99.880, 238.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Envelope protein E


Mass: 46323.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Cell line (production host): Schneider S2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: Q6DV88, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Protein Precursor Membrane Protein


Mass: 10194.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: peptide pr of the prM protein / Source: (gene. exp.) Yellow fever virus / Gene: prM / Cell line (production host): Schneider S2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: Q6DV88, UniProt: P03314*PLUS, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase

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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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 241 molecules

#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.2 M Li2SO4, 100mM TrisHCl pH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 63786 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.063 / Rrim(I) all: 0.111 / Net I/σ(I): 17
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4469 / CC1/2: 0.519 / Rpim(I) all: 0.814 / Rrim(I) all: 1.394 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5X

3c5x


Resolution: 2.7→29.717 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.69
RfactorNum. reflection% reflection
Rfree0.1863 3182 4.99 %
Rwork0.1615 --
obs0.1628 63742 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7606 0 292 205 8103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038055
X-RAY DIFFRACTIONf_angle_d0.67210935
X-RAY DIFFRACTIONf_dihedral_angle_d12.2372906
X-RAY DIFFRACTIONf_chiral_restr0.0281249
X-RAY DIFFRACTIONf_plane_restr0.0021358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.74670.37311600.34272962X-RAY DIFFRACTION95
2.7467-2.79660.40031540.31353023X-RAY DIFFRACTION95
2.7966-2.85040.32741550.28513051X-RAY DIFFRACTION95
2.8504-2.90850.29161480.2593003X-RAY DIFFRACTION95
2.9085-2.97170.28021590.24643032X-RAY DIFFRACTION95
2.9717-3.04070.2741700.2513027X-RAY DIFFRACTION95
3.0407-3.11670.26221520.22613063X-RAY DIFFRACTION95
3.1167-3.20080.22071570.20533013X-RAY DIFFRACTION95
3.2008-3.29490.19731670.19253014X-RAY DIFFRACTION95
3.2949-3.4010.19561660.17863017X-RAY DIFFRACTION95
3.401-3.52240.20281640.16863012X-RAY DIFFRACTION95
3.5224-3.66310.16131730.15873019X-RAY DIFFRACTION95
3.6631-3.82950.18681380.15283044X-RAY DIFFRACTION96
3.8295-4.03080.17041650.14913055X-RAY DIFFRACTION95
4.0308-4.28250.14551700.13213019X-RAY DIFFRACTION95
4.2825-4.61190.13021600.11543020X-RAY DIFFRACTION95
4.6119-5.07360.12881550.12193046X-RAY DIFFRACTION95
5.0736-5.80210.1511450.133041X-RAY DIFFRACTION95
5.8021-7.28910.17671600.14263044X-RAY DIFFRACTION95
7.2891-28.17270.19171630.14483045X-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)
13.0003-0.64291.83643.9462-1.17636.33440.13640.3313-0.10.044-0.066-0.37290.32540.2533-0.03690.43190.07810.03330.4040.08680.456420.310579.0059-18.9543
21.59640.067-0.33923.89241.03183.2599-0.01-0.0167-0.05550.179-0.247-0.18680.10810.01420.25870.4233-0.0305-0.05870.40550.07590.341911.37490.06167.0174
32.18151.8929-0.20833.4571-0.86350.98850.2360.05260.39890.062-0.3766-0.5427-0.42610.00450.23641.163-0.0269-0.06560.50360.13590.686316.402541.37340.8662
43.0996-0.62451.22214.72321.82446.11560.238-0.014-0.2097-0.6376-0.39560.622-0.1483-0.18350.18510.5528-0.0574-0.07640.5771-0.15020.51-21.235582.396118.4318
51.77940.523-0.07373.8599-1.29334.2282-0.0729-0.051-0.131-0.1664-0.26370.1957-0.0861-0.19440.32330.41120.073-0.07230.3933-0.09170.3513-8.76042.4355-6.8541
62.4156-2.7994-0.3613.56041.01251.42440.1962-0.09140.5008-0.3907-0.38510.4045-0.4067-0.09480.26851.14890.1025-0.11050.5363-0.1370.7536-12.781944.0830.4712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and ( (resid 1:45) OR (resid 139:183) OR (resid 280:407) ) )
2X-RAY DIFFRACTION2(chain A and ( (resid 64:120) OR (resid 231:247) ) ) OR (chain B)
3X-RAY DIFFRACTION3(chain A and ( (resid 46:63) OR (resid 121:138) OR (resid 184:230) OR (resid 248:279) ) )
4X-RAY DIFFRACTION4(chain D and ( (resid 1:45) OR (resid 139:183) OR (resid 280:407) ) )
5X-RAY DIFFRACTION5(chain D and ( (resid 64:120) OR (resid 231:247) ) ) OR (chain E)
6X-RAY DIFFRACTION6(chain D and ( (resid 46:63) OR (resid 121:138) OR (resid 184:230) OR (resid 248:279) ) )

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