[English] 日本語
Yorodumi
- PDB-4k67: Structure of an airborne transmissible avian influenza H5 hemaggl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k67
TitleStructure of an airborne transmissible avian influenza H5 hemagglutinin mutant from the influenza virus A/Indonesia/5/2005 complexed with human receptor analog LSTc
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / virus attachment / membrane fusion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
6'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level.
Authors: Zhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Qi, J. / Gao, G.F.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Refinement description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,63616
Polymers220,4598
Non-polymers3,1778
Water00
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,42212
Polymers165,3446
Non-polymers2,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area31550 Å2
ΔGint-123 kcal/mol
Surface area58310 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,42212
Polymers165,3446
Non-polymers2,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area31360 Å2
ΔGint-121 kcal/mol
Surface area58620 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03212
Polymers165,3446
Non-polymers2,6876
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 area32180 Å2
ΔGint-113 kcal/mol
Surface area58940 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03212
Polymers165,3446
Non-polymers2,6876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32220 Å2
ΔGint-108 kcal/mol
Surface area58950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.626, 70.626, 494.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 4:324 )
21chain C and (resseq 4:324 )
31chain E and (resseq 4:324 )
41chain G and (resseq 4:324 )
12chain B and (resseq 335:498 )
22chain D and (resseq 335:498 )
32chain F and (resseq 335:498 )
42chain H and (resseq 335:498 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERchain 'A' and (resseq 4:324 )AA4 - 3241 - 321
21GLNGLNSERSERchain 'C' and (resseq 4:324 )CC4 - 3241 - 321
31GLNGLNSERSERchain 'E' and (resseq 4:324 )EE4 - 3241 - 321
41GLNGLNSERSERchain 'G' and (resseq 4:324 )GG4 - 3241 - 321
12GLYGLYGLUGLUchain 'B' and (resseq 335:498 )BB335 - 4981 - 164
22GLYGLYGLUGLUchain 'D' and (resseq 335:498 )DD335 - 4981 - 164
32GLYGLYGLUGLUchain 'F' and (resseq 335:498 )FF335 - 4981 - 164
42GLYGLYGLUGLUchain 'H' and (resseq 335:498 )HH335 - 4981 - 164

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Hemagglutinin


Mass: 36203.953 Da / Num. of mol.: 4 / Fragment: UNP residues 17-326 / Mutation: H107Y, T160A, Q226L, G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#2: Protein
Hemagglutinin


Mass: 18910.838 Da / Num. of mol.: 4 / Fragment: UNP residues 347-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}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.: 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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 1500, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: -h,-k,l / Fraction: 0.2206
ReflectionResolution: 2.7→50 Å / Num. all: 72276 / Num. obs: 72276 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 51 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 95.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FK0

2fk0


Resolution: 2.7→49.117 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7704 / SU ML: 0.39 / σ(F): 1.97 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 3629 5.02 %RANDOM
Rwork0.2273 ---
all0.2287 72239 --
obs0.2287 72239 95.24 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.182 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 276.75 Å2 / Biso mean: 77.8937 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--8.6607 Å20 Å2-0 Å2
2---8.6607 Å20 Å2
3---17.3213 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 0 212 0 15692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516082
X-RAY DIFFRACTIONf_angle_d1.0821772
X-RAY DIFFRACTIONf_dihedral_angle_d18.7675926
X-RAY DIFFRACTIONf_chiral_restr0.1362358
X-RAY DIFFRACTIONf_plane_restr0.0032822
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2542X-RAY DIFFRACTIONPOSITIONAL0.051
12C2542X-RAY DIFFRACTIONPOSITIONAL0.051
13E2542X-RAY DIFFRACTIONPOSITIONAL0.156
14G2542X-RAY DIFFRACTIONPOSITIONAL0.171
21B1328X-RAY DIFFRACTIONPOSITIONAL0.102
22D1328X-RAY DIFFRACTIONPOSITIONAL0.102
23F1328X-RAY DIFFRACTIONPOSITIONAL0.175
24H1328X-RAY DIFFRACTIONPOSITIONAL0.153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6999-2.73540.36261020.351257794
2.7354-2.77290.3691440.3206267396
2.7729-2.81250.32941410.2998266997
2.8125-2.85450.33711380.3051264995
2.8545-2.89910.31891500.2824264097
2.8991-2.94660.32131510.2986265794
2.9466-2.99740.33221420.2829261296
2.9974-3.05190.31111190.2624272495
3.0519-3.11060.26831310.2508260695
3.1106-3.17410.23641500.2282260095
3.1741-3.24310.25171350.2341260494
3.2431-3.31850.29211310.252265496
3.3185-3.40150.30331470.2526259493
3.4015-3.49340.28071420.2349264495
3.4934-3.59620.24251390.2311257893
3.5962-3.71220.26871360.2394261193
3.7122-3.84490.29091250.2345260297
3.8449-3.99870.22571510.2113261294
3.9987-4.18060.25121460.2083264695
4.1806-4.40090.2341510.205267996
4.4009-4.67650.20191550.1944264596
4.6765-5.03720.23141470.1927266696
5.0372-5.54350.221490.2011260696
5.5435-6.34420.23041450.2014274799
6.3442-7.98750.21061250.1984277599
7.9875-49.12480.24451370.2124254091
Refinement TLS params.Method: refined / Origin x: 25.2967 Å / Origin y: 0.8509 Å / Origin z: 178.8035 Å
111213212223313233
T0.1105 Å2-0.0104 Å20.012 Å2-0.1146 Å2-0.0004 Å2--0.1061 Å2
L0 °2-0.0015 °20.0002 °2--0.0015 °20.0034 °2--0.0039 °2
S0.0081 Å °-0.0032 Å °-0.0052 Å °0.0039 Å °0.0026 Å °-0.0081 Å °0.0023 Å °0.0018 Å °-0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 324
2X-RAY DIFFRACTION1allA601 - 603
3X-RAY DIFFRACTION1allB335 - 498
4X-RAY DIFFRACTION1allC4 - 324
5X-RAY DIFFRACTION1allC601 - 603
6X-RAY DIFFRACTION1allD335 - 498
7X-RAY DIFFRACTION1allE4 - 324
8X-RAY DIFFRACTION1allE601 - 604
9X-RAY DIFFRACTION1allF335 - 498
10X-RAY DIFFRACTION1allG4 - 324
11X-RAY DIFFRACTION1allG601 - 604
12X-RAY DIFFRACTION1allH335 - 498

+
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