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- PDB-5wth: Cryo-EM structure for Hepatitis A virus complexed with FAB -

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Basic information

Entry
Database: PDB / ID: 5wth
TitleCryo-EM structure for Hepatitis A virus complexed with FAB
Components
  • FAB Heavy Chain
  • FAB Light Chain
  • Polyprotein
  • VP2
  • VP3
KeywordsVIRUS / HAV / Neutralizing mechanism / Receptor recognition / Viral entry
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHepatovirus A
Hepatitis A virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. ...Wang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. / Wang, J. / Fry, E.E. / Stuart, D.I. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation31570717 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.
Authors: Xiangxi Wang / Ling Zhu / Minghao Dang / Zhongyu Hu / Qiang Gao / Shuai Yuan / Yao Sun / Bo Zhang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Junzhi Wang / Elizabeth E Fry / David I Stuart / Zihe Rao /
Abstract: Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and ...Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.
History
DepositionDec 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Other
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Nov 6, 2019Group: Data collection / Experimental preparation / Other
Category: atom_sites / cell ...atom_sites / cell / em_sample_support / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _em_sample_support.grid_type / _em_software.name
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • 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
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Polyprotein
B: VP2
C: VP3
D: FAB Light Chain
E: FAB Heavy Chain


Theoretical massNumber of molelcules
Total (without water)130,5135
Polymers130,5135
Non-polymers00
Water00
1
A: Polyprotein
B: VP2
C: VP3
D: FAB Light Chain
E: FAB Heavy Chain
x 60


Theoretical massNumber of molelcules
Total (without water)7,830,761300
Polymers7,830,761300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Polyprotein
B: VP2
C: VP3
D: FAB Light Chain
E: FAB Heavy Chain
x 5


  • icosahedral pentamer
  • 653 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)652,56325
Polymers652,56325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein
B: VP2
C: VP3
D: FAB Light Chain
E: FAB Heavy Chain
x 6


  • icosahedral 23 hexamer
  • 783 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)783,07630
Polymers783,07630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Polyprotein
B: VP2
C: VP3
D: FAB Light Chain
E: FAB Heavy Chain
x 60


  • crystal asymmetric unit, crystal frame
  • 7.83 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)7,830,761300
Polymers7,830,761300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.95105651, -1.2E-7), (0.95105652, 0.30901699, 1.6E-7), (-1.2E-7, -1.7E-7, 1)
3generate(-0.80901699, -0.58778525, -3.0E-7), (0.58778526, -0.809017, 1.0E-7), (-3.2E-7, -1.1E-7, 1)
4generate(-0.809017, 0.58778525, -3.0E-7), (-0.58778526, -0.80901699, -1.0E-7), (-3.2E-7, 1.0E-7, 1)
5generate(0.30901699, 0.95105651, -1.2E-7), (-0.95105652, 0.309017, -1.6E-7), (-1.2E-7, 1.7E-7, 1)
6generate(-0.94721369, -0.1624597, 0.27639297), (-0.1624597, -0.5, -0.85065084), (0.27639296, -0.85065083, 0.44721369)
7generate(-0.44721352, 0.85065089, 0.27639305), (-0.52573097, -0.8506509), (-0.72360695, -0.52573096, 0.44721352)
8generate(0.67082047, 0.68819086, 0.27639324), (-0.1624597, 0.5, -0.85065084), (-0.72360676, 0.52573123, 0.44721352)
9generate(0.86180331, -0.42532555, 0.27639327), (0.42532556, 0.309017, -0.85065074), (0.27639328, 0.85065072, 0.44721369)
10generate(-0.1381968, -0.95105651, 0.2763931), (0.42532556, -0.30901699, -0.85065074), (0.89442709, -1.7E-7, 0.44721379)
11generate(-0.8618033, -0.42532554, -0.27639327), (-0.42532556, 0.30901699, 0.85065074), (-0.27639328, 0.85065073, -0.44721369)
12generate(-0.67082047, 0.68819087, -0.27639324), (0.1624597, 0.5, 0.85065084), (0.72360676, 0.52573123, -0.44721352)
13generate(0.44721352, 0.85065089, -0.27639305), (0.52573097, 0.8506509), (0.72360696, -0.52573096, -0.44721352)
14generate(0.94721369, -0.16245971, -0.27639296), (0.1624597, -0.5, 0.85065084), (-0.27639296, -0.85065083, -0.44721369)
15generate(0.1381968, -0.95105651, -0.2763931), (-0.42532556, -0.309017, 0.85065074), (-0.89442709, -1.6E-7, -0.44721379)
16generate(0.809017, 0.58778524, 3.0E-7), (0.58778526, -0.809017, 1.0E-7), (3.2E-7, 1.0E-7, -1)
17generate(0.80901699, -0.58778525, 3.0E-7), (-0.58778526, -0.80901699, -1.0E-7), (3.2E-7, -1.0E-7, -1)
18generate(-0.309017, -0.95105651, 1.2E-7), (-0.95105653, 0.309017, -1.6E-7), (1.2E-7, -1.6E-7, -1)
19generate(-1), (1), (-1)
20generate(-0.30901699, 0.95105651, 1.2E-7), (0.95105652, 0.30901699, 1.6E-7), (1.2E-7, 1.7E-7, -1)
21generate(-0.1381968, -0.42532555, 0.89442709), (0.95105653, -0.309017, 1.6E-7), (0.2763931, 0.85065072, 0.4472138)
22generate(-0.4472139, 0.89442704), (-1), (0.89442703, 0.4472139)
23generate(-0.13819681, 0.42532554, 0.89442709), (-0.95105652, -0.30901699, -1.6E-7), (0.2763931, -0.85065073, 0.4472138)
24generate(0.36180336, 0.26286564, 0.89442718), (-0.58778526, 0.809017, -1.0E-7), (-0.72360681, -0.52573106, 0.44721363)
25generate(0.36180337, -0.26286564, 0.89442718), (0.58778526, 0.80901699, 1.0E-7), (-0.72360681, 0.52573106, 0.44721363)
26generate(0.44721351, -0.52573097, 0.72360695), (-0.85065091, 0.52573097), (-0.27639305, -0.85065089, -0.44721351)
27generate(-0.36180338, -0.58778525, 0.72360681), (-0.26286565, 0.80901699, 0.52573107), (-0.89442718, -1.0E-7, -0.44721362)
28generate(-0.67082047, 0.16245971, 0.72360676), (0.68819087, 0.5, 0.52573123), (-0.27639324, 0.85065083, -0.44721351)
29generate(-0.05278665, 0.68819086, 0.72360687), (0.68819087, -0.5, 0.52573123), (0.72360687, 0.52573123, -0.44721335)
30generate(0.63819635, 0.26286564, 0.72360698), (-0.26286565, -0.80901699, 0.52573107), (0.72360699, -0.52573106, -0.44721335)
31generate(0.05278665, 0.68819087, -0.72360687), (-0.68819087, -0.5, -0.52573123), (-0.72360687, 0.52573123, 0.44721335)
32generate(0.67082047, 0.1624597, -0.72360676), (-0.68819087, 0.5, -0.52573123), (0.27639324, 0.85065083, 0.44721351)
33generate(0.36180338, -0.58778524, -0.72360681), (0.26286565, 0.80901699, -0.52573107), (0.89442718, -1.0E-7, 0.44721362)
34generate(-0.44721351, -0.52573096, -0.72360695), (0.85065091, -0.52573097), (0.27639305, -0.85065089, 0.44721351)
35generate(-0.63819635, 0.26286564, -0.72360698), (0.26286565, -0.80901699, -0.52573107), (-0.72360699, -0.52573106, 0.44721335)
36generate(-0.36180336, 0.26286565, -0.89442718), (0.58778526, 0.80901699, 1.0E-7), (0.72360681, -0.52573106, -0.44721363)
37generate(0.13819681, 0.42532554, -0.89442709), (0.95105653, -0.309017, 1.6E-7), (-0.2763931, -0.85065072, -0.4472138)
38generate(0.4472139, -0.89442704), (-1), (-0.89442703, -0.4472139)
39generate(0.1381968, -0.42532554, -0.89442709), (-0.95105652, -0.30901699, -1.6E-7), (-0.2763931, 0.85065073, -0.4472138)
40generate(-0.36180337, -0.26286564, -0.89442718), (-0.58778526, 0.809017, -1.0E-7), (0.72360681, 0.52573106, -0.44721363)
41generate(-0.1381968, 0.95105651, 0.27639311), (-0.42532556, -0.30901699, 0.85065075), (0.89442709, 1.6E-7, 0.4472138)
42generate(0.8618033, 0.42532554, 0.27639327), (-0.42532556, 0.30901699, 0.85065075), (0.27639327, -0.85065073, 0.44721369)
43generate(0.67082047, -0.68819087, 0.27639324), (0.1624597, 0.5, 0.85065084), (-0.72360676, -0.52573123, 0.44721352)
44generate(-0.44721352, -0.85065089, 0.27639305), (0.52573097, 0.85065091), (-0.72360695, 0.52573096, 0.44721352)
45generate(-0.94721369, 0.1624597, 0.27639297), (0.1624597, -0.5, 0.85065084), (0.27639296, 0.85065083, 0.44721369)
46generate(0.05278666, -0.68819087, -0.72360686), (0.68819087, -0.5, 0.52573123), (-0.72360686, -0.52573123, 0.44721335)
47generate(-0.63819635, -0.26286564, -0.72360698), (-0.26286565, -0.80901699, 0.52573107), (-0.72360699, 0.52573106, 0.44721335)
48generate(-0.44721352, 0.52573097, -0.72360695), (-0.85065091, 0.52573097), (0.27639304, 0.85065089, 0.44721352)
49generate(0.36180337, 0.58778525, -0.72360681), (-0.26286565, 0.80901699, 0.52573107), (0.89442717, 1.0E-7, 0.44721362)
50generate(0.67082048, -0.1624597, -0.72360676), (0.68819087, 0.5, 0.52573123), (0.27639324, -0.85065083, 0.44721352)
51generate(-0.36180337, 0.58778525, 0.72360681), (0.26286565, 0.809017, -0.52573107), (-0.89442717, 1.1E-7, -0.44721362)
52generate(0.44721352, 0.52573096, 0.72360695), (0.85065091, -0.52573097), (-0.27639304, 0.85065089, -0.44721352)
53generate(0.63819635, -0.26286565, 0.72360698), (0.26286565, -0.80901699, -0.52573107), (0.72360699, 0.52573106, -0.44721335)
54generate(-0.05278665, -0.68819087, 0.72360686), (-0.68819087, -0.5, -0.52573123), (0.72360687, -0.52573123, -0.44721335)
55generate(-0.67082048, -0.1624597, 0.72360676), (-0.68819088, 0.5, -0.52573123), (-0.27639324, -0.85065083, -0.44721352)
56generate(0.44721352, -0.85065089, -0.27639305), (-0.52573097, -0.85065091), (0.72360695, 0.52573096, -0.44721352)
57generate(-0.67082047, -0.68819086, -0.27639324), (-0.1624597, 0.5, -0.85065084), (0.72360676, -0.52573123, -0.44721352)
58generate(-0.8618033, 0.42532555, -0.27639327), (0.42532556, 0.309017, -0.85065075), (-0.27639327, -0.85065072, -0.44721369)
59generate(0.1381968, 0.95105651, -0.27639311), (0.42532556, -0.30901699, -0.85065075), (-0.89442709, 1.7E-7, -0.4472138)
60generate(0.94721369, 0.1624597, -0.27639297), (-0.1624597, -0.5, -0.85065084), (-0.27639296, 0.85065083, -0.44721369)

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Components

#1: Protein Polyprotein


Mass: 30820.629 Da / Num. of mol.: 1 / Fragment: UNP residues 20-289 / Source method: isolated from a natural source / Source: (natural) Hepatovirus A / Organ: Homo sapiens / References: UniProt: P08617*PLUS
#2: Protein VP2


Mass: 24898.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hepatitis A virus / Organ: Homo sapiens / References: UniProt: P08617*PLUS
#3: Protein VP3


Mass: 27835.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hepatitis A virus / Organ: Homo sapiens / References: UniProt: P08617*PLUS
#4: Antibody FAB Light Chain


Mass: 23283.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody FAB Heavy Chain


Mass: 23674.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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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: Hepatitis A virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 6 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis A virus
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: vero
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: PBS Buffer
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: blot for 3s seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 500
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionEMAN2 e2boxer.py was used to automatically select particle images
4Gctf3CTF correction
7CHIMERAmodel fitting
10RELION1.3final Euler assignment
12RELION1.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2200 / Num. of class averages: 40 / Symmetry type: POINT
Atomic model buildingB value: 150 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

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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

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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

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