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- PDB-4c2i: Cryo-EM structure of Dengue virus serotype 1 complexed with Fab f... -

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Basic information

Entry
Database: PDB / ID: 4c2i
TitleCryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody 1F4
Components
  • ENVELOPE PROTEINViral envelope
  • HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
  • LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
  • POLYPROTEINProteolysis
KeywordsVIRUS / E PROTEINS / NEUTRALIZATION
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / 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 / 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 / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Genome polyprotein / Envelope protein E
Similarity search - Component
Biological speciesDENGUE VIRUS 1
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
Model type detailsCA ATOMS ONLY, CHAIN A, C, E, B, D, F, H, M, L, N
AuthorsFibriansah, G. / Tan, J.L. / de Alwis, R. / Smith, S.A. / Ng, T.-S. / Kostyuchenko, V.A. / Ibarra, K.D. / Harris, E. / de Silva, A. / Crowe Junior, J.E. / Lok, S.-M.
CitationJournal: EMBO Mol Med / Year: 2014
Title: A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface.
Authors: Guntur Fibriansah / Joanne L Tan / Scott A Smith / Adamberage R de Alwis / Thiam-Seng Ng / Victor A Kostyuchenko / Kristie D Ibarra / Jiaqi Wang / Eva Harris / Aravinda de Silva / James E Crowe / Shee-Mei Lok /
Abstract: Dengue virus (DENV), which consists of four serotypes (DENV1-4), infects over 400 million people annually. Previous studies have indicated most human monoclonal antibodies (HMAbs) from dengue ...Dengue virus (DENV), which consists of four serotypes (DENV1-4), infects over 400 million people annually. Previous studies have indicated most human monoclonal antibodies (HMAbs) from dengue patients are cross-reactive and poorly neutralizing. Rare neutralizing HMAbs are usually serotype-specific and bind to quaternary structure-dependent epitopes. We determined the structure of DENV1 complexed with Fab fragments of a highly potent HMAb 1F4 to 6 Å resolution by cryo-EM. Although HMAb 1F4 appeared to bind to virus and not E proteins in ELISAs in the previous study, our structure showed that the epitope is located within an envelope (E) protein monomer, and not across neighboring E proteins. The Fab molecules bind to domain I (DI), and DI-DII hinge of the E protein. We also showed that HMAb 1F4 can neutralize DENV at different stages of viral entry in a cell type and receptor dependent manner. The structure reveals the mechanism by which this potent and specific antibody blocks viral infection.
History
DepositionAug 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Other / Source and taxonomy
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2442
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  • Superimposition on EM map
  • EMDB-2442
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Structure viewerMolecule:
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Assembly

Deposited unit
A: ENVELOPE PROTEIN
B: POLYPROTEIN
C: ENVELOPE PROTEIN
D: POLYPROTEIN
E: ENVELOPE PROTEIN
F: POLYPROTEIN
H: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
L: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
M: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
N: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,28716
Polymers286,53810
Non-polymers2,7506
Water0
1
A: ENVELOPE PROTEIN
B: POLYPROTEIN
C: ENVELOPE PROTEIN
D: POLYPROTEIN
E: ENVELOPE PROTEIN
F: POLYPROTEIN
H: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
L: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
M: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
N: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)17,357,240960
Polymers17,192,264600
Non-polymers164,976360
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: ENVELOPE PROTEIN
B: POLYPROTEIN
C: ENVELOPE PROTEIN
D: POLYPROTEIN
E: ENVELOPE PROTEIN
F: POLYPROTEIN
H: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
L: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
M: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
N: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
hetero molecules
x 5


  • icosahedral pentamer
  • 1.45 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,446,43780
Polymers1,432,68950
Non-polymers13,74830
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: ENVELOPE PROTEIN
B: POLYPROTEIN
C: ENVELOPE PROTEIN
D: POLYPROTEIN
E: ENVELOPE PROTEIN
F: POLYPROTEIN
H: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
L: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
M: HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4
N: LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.74 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,735,72496
Polymers1,719,22660
Non-polymers16,49836
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(-0.638197, 0.262866, -0.723607), (0.262866, -0.809017, -0.525731), (-0.723607, -0.525731, 0.447214)
3generate(-0.447214, 0.525731, -0.723607), (-0.850651, 0.525731), (0.276393, 0.850651, 0.447214)
4generate(-0.361803, 0.262866, -0.894427), (0.587785, 0.809017), (0.723607, -0.525731, -0.447214)
5generate(-0.67082, 0.688191, -0.276393), (0.16246, 0.5, 0.850651), (0.723607, 0.525731, -0.447214)
6generate(0.138197, 0.425325, -0.894427), (0.951057, -0.309017), (-0.276393, -0.850651, -0.447214)
7generate(-0.638197, -0.262866, -0.723607), (-0.262866, -0.809017, 0.525731), (-0.723607, 0.525731, 0.447214)
8generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)
9generate(-0.138197, 0.951057, 0.276393), (-0.425325, -0.309017, 0.850651), (0.894427, 0.447214)
10generate(0.67082, -0.16246, -0.723607), (0.688191, 0.5, 0.525731), (0.276393, -0.850651, 0.447214)
11generate(0.447214, 0.850651, -0.276393), (0.525731, 0.850651), (0.723607, -0.525731, -0.447214)
12generate(0.052786, -0.688191, -0.723607), (0.688191, -0.5, 0.525731), (-0.723607, -0.525731, 0.447214)
13generate(-0.947214, 0.16246, 0.276393), (0.16246, -0.5, 0.850651), (0.276393, 0.850651, 0.447214)
14generate(-0.138197, -0.425325, 0.894427), (0.951057, -0.309017), (0.276393, 0.850651, 0.447214)
15generate(0.638197, 0.262866, 0.723607), (-0.262866, -0.809017, 0.525731), (0.723607, -0.525731, -0.447214)
16generate(0.67082, -0.688191, 0.276393), (0.16246, 0.5, 0.850651), (-0.723607, -0.525731, 0.447214)
17generate(0.947214, -0.16246, -0.276393), (0.16246, -0.5, 0.850651), (-0.276393, -0.850651, -0.447214)
18generate(-0.447214, -0.850651, 0.276393), (0.525731, 0.850651), (-0.723607, 0.525731, 0.447214)
19generate(-0.052786, 0.688191, 0.723607), (0.688191, -0.5, 0.525731), (0.723607, 0.525731, -0.447214)
20generate(0.447214, 0.525731, 0.723607), (0.850651, -0.525731), (-0.276393, 0.850651, -0.447214)
21generate(0.809017, -0.587785), (-0.587785, -0.809017), (-1)
22generate(-0.361803, -0.587785, 0.723607), (-0.262866, 0.809017, 0.525731), (-0.894427, -0.447214)
23generate(0.138197, -0.951057, -0.276393), (-0.425325, -0.309017, 0.850651), (-0.894427, -0.447214)
24generate(-0.67082, 0.16246, 0.723607), (0.688191, 0.5, 0.525731), (-0.276393, 0.850651, -0.447214)
25generate(0.809017, 0.587785), (0.587785, -0.809017), (-1)
26generate(0.138197, 0.951057, -0.276393), (0.425325, -0.309017, -0.850651), (-0.894427, -0.447214)
27generate(0.138197, -0.425325, -0.894427), (-0.951057, -0.309017), (-0.276393, 0.850651, -0.447214)
28generate(-1), (1), (-1)
29generate(-0.861803, -0.425325, -0.276393), (-0.425325, 0.309017, 0.850651), (-0.276393, 0.850651, -0.447214)
30generate(-0.309017, 0.951057), (0.951057, 0.309017), (-1)
31generate(0.447214, -0.894427), (-1), (-0.894427, -0.447214)
32generate(0.361803, 0.587785, -0.723607), (-0.262866, 0.809017, 0.525731), (0.894427, 0.447214)
33generate(-0.447214, -0.525731, -0.723607), (0.850651, -0.525731), (0.276393, -0.850651, 0.447214)
34generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)
35generate(-0.947214, -0.16246, 0.276393), (-0.16246, -0.5, -0.850651), (0.276393, -0.850651, 0.447214)
36generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)
37generate(0.361803, -0.587785, -0.723607), (0.262866, 0.809017, -0.525731), (0.894427, 0.447214)
38generate(-0.361803, -0.262866, -0.894427), (-0.587785, 0.809017), (0.723607, 0.525731, -0.447214)
39generate(-0.861803, 0.425325, -0.276393), (0.425325, 0.309017, -0.850651), (-0.276393, -0.850651, -0.447214)
40generate(0.052786, 0.688191, -0.723607), (-0.688191, -0.5, -0.525731), (-0.723607, 0.525731, 0.447214)
41generate(-0.447214, 0.850651, 0.276393), (-0.525731, -0.850651), (-0.723607, -0.525731, 0.447214)
42generate(0.67082, 0.16246, -0.723607), (-0.688191, 0.5, -0.525731), (0.276393, 0.850651, 0.447214)
43generate(-0.67082, -0.688191, -0.276393), (-0.16246, 0.5, -0.850651), (0.723607, -0.525731, -0.447214)
44generate(-0.309017, -0.951057), (-0.951057, 0.309017), (-1)
45generate(-0.361803, 0.587785, 0.723607), (0.262866, 0.809017, -0.525731), (-0.894427, -0.447214)
46generate(0.947214, 0.16246, -0.276393), (-0.16246, -0.5, -0.850651), (-0.276393, 0.850651, -0.447214)
47generate(0.67082, 0.688191, 0.276393), (-0.16246, 0.5, -0.850651), (-0.723607, 0.525731, 0.447214)
48generate(0.447214, -0.850651, -0.276393), (-0.525731, -0.850651), (0.723607, 0.525731, -0.447214)
49generate(-0.67082, -0.16246, 0.723607), (-0.688191, 0.5, -0.525731), (-0.276393, -0.850651, -0.447214)
50generate(0.447214, -0.525731, 0.723607), (-0.850651, 0.525731), (-0.276393, -0.850651, -0.447214)
51generate(0.361803, -0.262866, 0.894427), (0.587785, 0.809017), (-0.723607, 0.525731, 0.447214)
52generate(0.638197, -0.262866, 0.723607), (0.262866, -0.809017, -0.525731), (0.723607, 0.525731, -0.447214)
53generate(0.861803, -0.425325, 0.276393), (0.425325, 0.309017, -0.850651), (0.276393, 0.850651, 0.447214)
54generate(-0.052786, -0.688191, 0.723607), (-0.688191, -0.5, -0.525731), (0.723607, -0.525731, -0.447214)
55generate(0.361803, 0.262866, 0.894427), (-0.587785, 0.809017), (-0.723607, -0.525731, 0.447214)
56generate(0.861803, 0.425325, 0.276393), (-0.425325, 0.309017, 0.850651), (0.276393, -0.850651, 0.447214)
57generate(0.309017, -0.951057), (0.951057, 0.309017), (1)
58generate(-0.447214, 0.894427), (-1), (0.894427, 0.447214)
59generate(-0.138197, -0.951057, 0.276393), (0.425325, -0.309017, -0.850651), (0.894427, 0.447214)
60generate(-0.138197, 0.425325, 0.894427), (-0.951057, -0.309017), (0.276393, -0.850651, 0.447214)

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein ENVELOPE PROTEIN / Viral envelope / Coordinate model: Cα atoms only


Mass: 53894.797 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: STRAIN PVP159 / Source: (natural) DENGUE VIRUS 1 / References: UniProt: Q7TGE4
#2: Protein POLYPROTEIN / Proteolysis / Coordinate model: Cα atoms only


Mass: 8081.494 Da / Num. of mol.: 3 / Fragment: MEMBRANE PROTEIN, RESIDUES 206-280 / Source method: isolated from a natural source / Details: STRAIN PVP159 / Source: (natural) DENGUE VIRUS 1 / References: UniProt: G3F5K5

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Antibody , 2 types, 4 molecules HMLN

#3: Antibody HEAVY CHAIN FAB FRAGMENT OF ANTIBODY 1F4 / Coordinate model: Cα atoms only


Mass: 24835.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: B CELLS
#4: Antibody LIGHT CHAIN FAB FRAGMENT OF ANTIBODY 1F4 / Coordinate model: Cα atoms only


Mass: 25468.553 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: B CELLS

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Sugars , 3 types, 6 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 3
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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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Details

Sequence detailsDENGUE VIRUS SEROTYPE 1 STRAIN PVP159 USED IN THIS STRUCTURAL STUDY IS A LABORATORY STRAIN. IT HAS ...DENGUE VIRUS SEROTYPE 1 STRAIN PVP159 USED IN THIS STRUCTURAL STUDY IS A LABORATORY STRAIN. IT HAS SEVERAL MUTATIONS COMPARED TO THAT DESCRIBED IN Q7TGE4. IT HAS BEEN SEQUENCED AS A PART OF POLYPROTEIN ENCODED BY THE VIRAL GENOME.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DENGUE VIRUS SEROTYPE 1 WITH FAB FRAGMENTS OF HUMAN MONOCLONAL ANTIBODY 1F4
Type: VIRUS
Buffer solutionName: 12 MM TRIS-HCL PH 8.0, 120 MM NACL AND 1 MM EDTA / pH: 8 / Details: 12 MM TRIS-HCL PH 8.0, 120 MM NACL AND 1 MM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT WITH FILTER PAPER FOR 2 S BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 14, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 17.5 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)
Image scansNum. digital images: 254
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2MPSA3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 6 Å / Num. of particles: 10270 / Nominal pixel size: 1 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2442. (DEPOSITION ID: 11902).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 4AZX

4azx
PDB Unreleased entry

RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 182 0 2761

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