[English] 日本語
Yorodumi
- PDB-5swz: Crystal Structure of NP1-B17 TCR-H2Db-NP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5swz
TitleCrystal Structure of NP1-B17 TCR-H2Db-NP complex
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NP1-B17 TCR alpha chain
  • NP1-B17 TCR beta chain
  • influenza NP366 epitope
KeywordsIMMUNE SYSTEM / H2Db / influenza / NP366 / reversed docking / naive T cell / NP1-B17 TCR / TCR / T cell
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / viral penetration into host nucleus / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / host cell / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / ribonucleoprotein complex / external side of plasma membrane / symbiont entry into host cell / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsGras, S. / Del Campo, C.M. / Farenc, C. / Josephs, T.M. / Rossjohn, J.
CitationJournal: Immunity / Year: 2016
Title: Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response.
Authors: Gras, S. / Chadderton, J. / Del Campo, C.M. / Farenc, C. / Wiede, F. / Josephs, T.M. / Sng, X.Y. / Mirams, M. / Watson, K.A. / Tiganis, T. / Quinn, K.M. / Rossjohn, J. / La Gruta, N.L.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: influenza NP366 epitope
D: NP1-B17 TCR alpha chain
E: NP1-B17 TCR beta chain
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: influenza NP366 epitope
I: NP1-B17 TCR alpha chain
J: NP1-B17 TCR beta chain
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: influenza NP366 epitope
N: NP1-B17 TCR alpha chain
O: NP1-B17 TCR beta chain
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: influenza NP366 epitope
S: NP1-B17 TCR alpha chain
T: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,18731
Polymers384,56820
Non-polymers61811
Water9,584532
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: influenza NP366 epitope
D: NP1-B17 TCR alpha chain
E: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3578
Polymers96,1425
Non-polymers2153
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: influenza NP366 epitope
I: NP1-B17 TCR alpha chain
J: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1887
Polymers96,1425
Non-polymers462
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: influenza NP366 epitope
N: NP1-B17 TCR alpha chain
O: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3578
Polymers96,1425
Non-polymers2153
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: influenza NP366 epitope
S: NP1-B17 TCR alpha chain
T: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2848
Polymers96,1425
Non-polymers1423
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.231, 100.185, 469.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 16 molecules AFKPBGLQDINSEJOT

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32470.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#4: Protein
NP1-B17 TCR alpha chain


Mass: 23117.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein
NP1-B17 TCR beta chain


Mass: 27868.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Protein/peptide , 1 types, 4 molecules CHMR

#3: Protein/peptide
influenza NP366 epitope


Mass: 1026.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS

-
Non-polymers , 3 types, 543 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.49 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 17% 3350, 0.2 KNaTartrate, 0.1 BTP 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→38.8 Å / Biso Wilson estimate: 66.83 Å2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.208 / Num. measured all: 272722 / Num. unique all: 18435 / CC1/2: 0.613 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Rsym value: 0.047 / Net I/σ(I) obs: 2 / Rejects: 0 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUU, 1KGC

4huu

1kgc


Resolution: 2.65→38.8 Å / Cor.coef. Fo:Fc: 0.9015 / Cor.coef. Fo:Fc free: 0.8738 / SU R Cruickshank DPI: 0.711 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.701 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 6523 5.12 %RANDOM
Rwork0.2257 ---
obs0.2269 127456 99.98 %-
Displacement parametersBiso mean: 72.61 Å2
Baniso -1Baniso -2Baniso -3
1--6.0916 Å20 Å20 Å2
2---5.9491 Å20 Å2
3---12.0408 Å2
Refine analyzeLuzzati coordinate error obs: 0.482 Å
Refinement stepCycle: LAST / Resolution: 2.65→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26494 0 31 575 27100
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00727272HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9537068HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes749HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3917HARMONIC5
X-RAY DIFFRACTIONt_it27272HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion21.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact27932SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3181 472 5.07 %
Rwork0.2952 8846 -
all0.2964 9318 -
obs--99.98 %
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)
11.87340.0392-1.51340.3840.09452.57640.0188-0.01640.14750.05130.013-0.13540.04860.2911-0.0317-0.07920.03960.00810.00320.12-0.082763.8336-3.3582-26.5018
22.64990.11720.00070.3632-0.30873.11860.01550.1476-0.0533-0.10590.01450.0579-0.0001-0.0111-0.030.00780.13720.01060.09940.1273-0.13952.392-3.5179-42.5299
31.4198-0.2268-1.14720.47720.05953.2299-0.0343-0.0630.2571-0.02110.07770.0597-0.0851-0.0773-0.0433-0.06620.002-0.0026-0.0370.12620.06117.3678-6.594917.6841
41.0713-0.3324-1.00120.8671-1.31594.1351-0.0155-0.14390.09850.04670.06830.0067-0.14230.1259-0.0528-0.0778-0.0404-0.0347-0.0210.0366-0.12436.6774-8.708624.3642
50.0162-0.91060.72032.4644-2.29472.0406-0.05920.0361-0.08660.0297-0.10820.02430.26360.28130.1674-0.06650.14920.14940.21650.1447-0.19124.3263-47.7013-92.0446
60.9751-1.1724-0.93560.91840.33442.70670.0197-0.13770.09380.1707-0.0235-0.1022-0.00680.10760.0039-0.01240.14790.15190.24220.1516-0.164923.795-36.2468-75.9837
70.17570.02560.7811.3625-1.31122.76580.0314-0.09610.129-0.2062-0.04-0.0362-0.08170.0170.0086-0.04770.06410.1520.10490.0741-0.005126.5408-1.5613-135.191
82.01050.1901-2.42750.91920.55255.7657-0.0108-0.1518-0.1768-0.42250.159-0.082-0.2728-0.0271-0.1481-0.01760.10480.1275-0.03640.0181-0.232930.5188-19.6554-142.44
90.18390.21870.71260.8388-0.66372.9013-0.0455-0.1157-0.1291-0.25110.070.2420.1224-0.236-0.0245-0.02930.0352-0.03560.0122-0.0619-0.0539-13.0611-25.7993-118.511
101.44421.7329-0.92581.753-0.03872.8385-0.0140.07780.1116-0.1466-0.05610.1131-0.08230.00250.0701-0.01850.1071-0.07730.0352-0.0646-0.0834-2.3513-13.3744-129.717
110.5286-0.71650.65850.0356-0.62873.99520.0127-0.2478-0.0579-0.1540.0534-0.0631-0.04820.1428-0.066-0.0674-0.14730.03940.1945-0.0069-0.110511.8993-12.9284-60.826
120.1897-0.287-0.3340.26710.16655.18130.0162-0.1328-0.0268-0.05060.0348-0.06410.13420.0729-0.051-0.1693-0.00870.02670.15510.0274-0.0946-4.4496-24.7064-60.7412
130.7278-0.22320.12151.30660.75312.5656-0.0173-0.13920.2490.1209-0.02580.0358-0.11360.17470.0431-0.1005-0.07250.099-0.04380.0140.124439.827734.8247-5.2079
141.09410.2374-1.34110.0008-0.21321.8381-0.001-0.16130.05390.12290.01910.058-0.0246-0.117-0.0181-0.0549-0.09240.13110.16770.0145-0.042728.272523.172510.7948
150.5325-0.1149-1.15430.62460.63724.24510.02850.1283-0.1186-0.1351-0.0340.10430.0707-0.08520.0055-0.12250.0658-0.03310.07320.1090.075130.080110.2606-59.5446
160.3928-0.0081-1.32940.19290.42566.35710.11210.08930.0276-0.0771-0.1350.0534-0.22080.05460.0229-0.00370.14740.0191-0.05420.145-0.062442.545926.2469-57.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|277 }A1 - 277
2X-RAY DIFFRACTION2{ B|1 - B|99 }B1 - 99
3X-RAY DIFFRACTION3{ D|1 - D|216 }D1 - 216
4X-RAY DIFFRACTION4{ E|3 - E|255 }E3 - 255
5X-RAY DIFFRACTION5{ F|1 - F|277 }F1 - 277
6X-RAY DIFFRACTION6{ G|1 - G|99 }G1 - 99
7X-RAY DIFFRACTION7{ I|1 - I|205 }I1 - 205
8X-RAY DIFFRACTION8{ J|3 - J|255 }J3 - 255
9X-RAY DIFFRACTION9{ K|1 - K|277 }K1 - 277
10X-RAY DIFFRACTION10{ L|1 - L|99 }L1 - 99
11X-RAY DIFFRACTION11{ N|1 - N|217 }N1 - 217
12X-RAY DIFFRACTION12{ O|3 - O|256 }O3 - 256
13X-RAY DIFFRACTION13{ P|1 - P|271 }P1 - 271
14X-RAY DIFFRACTION14{ Q|2 - Q|99 }Q2 - 99
15X-RAY DIFFRACTION15{ S|1 - S|217 }S1 - 217
16X-RAY DIFFRACTION16{ T|3 - T|254 }T3 - 254

+
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