[English] 日本語
Yorodumi
- PDB-2zsw: Crystal structure of H-2Kb in complex with the Q600Y variant of J... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zsw
TitleCrystal structure of H-2Kb in complex with the Q600Y variant of JHMV epitope S598
Components
  • 8-mer peptide from spike glycoprotein
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / Ig Fold / protein-protein interactions / subdominant epitope / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted
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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / 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 / peptide antigen binding / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / receptor-mediated virion attachment to host cell / defense response to bacterium / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / cytosol
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / 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, K-B alpha chain / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTheodossis, A. / Dunstone, M.A. / Rossjohn, J.
CitationJournal: Plos Pathog. / Year: 2008
Title: Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant.
Authors: Butler, N.S. / Theodossis, A. / Webb, A.I. / Nastovska, R. / Ramarathinam, S.H. / Dunstone, M.A. / Rossjohn, J. / Purcell, A.W. / Perlman, S.
History
DepositionSep 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
E: H-2 class I histocompatibility antigen, K-B alpha chain
C: H-2 class I histocompatibility antigen, K-B alpha chain
G: H-2 class I histocompatibility antigen, K-B alpha chain
H: Beta-2-microglobulin
F: Beta-2-microglobulin
B: Beta-2-microglobulin
D: Beta-2-microglobulin
M: 8-mer peptide from spike glycoprotein
N: 8-mer peptide from spike glycoprotein
O: 8-mer peptide from spike glycoprotein
P: 8-mer peptide from spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)179,02112
Polymers179,02112
Non-polymers00
Water2,684149
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
M: 8-mer peptide from spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,7553
Polymers44,7553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-13 kcal/mol
Surface area18880 Å2
MethodPISA
2
E: H-2 class I histocompatibility antigen, K-B alpha chain
F: Beta-2-microglobulin
N: 8-mer peptide from spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,7553
Polymers44,7553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-15 kcal/mol
Surface area19290 Å2
MethodPISA
3
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
O: 8-mer peptide from spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,7553
Polymers44,7553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-15 kcal/mol
Surface area18610 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, K-B alpha chain
H: Beta-2-microglobulin
P: 8-mer peptide from spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,7553
Polymers44,7553
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-14 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.711, 90.147, 91.969
Angle α, β, γ (deg.)81.11, 70.58, 68.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13M
23N
33O
43P

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2771 - 277
21GLYGLYPROPROCC1 - 2771 - 277
31GLYGLYPROPROEB1 - 2771 - 277
41GLYGLYPROPROGD1 - 2771 - 277
12GLNGLNMETMETBG2 - 992 - 99
22GLNGLNMETMETDH2 - 992 - 99
32GLNGLNMETMETFF2 - 992 - 99
42GLNGLNMETMETHE2 - 992 - 99
13ARGARGILEILEMI1 - 81 - 8
23ARGARGILEILENJ1 - 81 - 8
33ARGARGILEILEOK1 - 81 - 8
43ARGARGILEILEPL1 - 81 - 8

NCS ensembles :
ID
1
2
3

-
Components

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


Mass: 32068.777 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide
8-mer peptide from spike glycoprotein


Mass: 982.158 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mouse Hepatitis Virus JHM strain
References: UniProt: P11225*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS Q3Y MUTANT OF L-ALPHA-AMINOBUTYRIC ACID SUBSTITUTED IN CHAINS H, F, B, D

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M cacodylate, 13% PEG 8K, 0.2M Ca(OAc)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→27 Å / Num. obs: 44395 / % possible obs: 95.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4426 / % possible all: 85.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G7Q

1g7q


Resolution: 2.8→27 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 33.882 / SU ML: 0.318 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 2240 5.1 %RANDOM
Rwork0.21189 ---
obs0.214 42022 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.048 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å21.9 Å2-2.48 Å2
2---3.06 Å2-0.95 Å2
3---4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12156 0 0 149 12305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02112543
X-RAY DIFFRACTIONr_angle_refined_deg1.41.93917115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9151524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21723.682603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.352151905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651577
X-RAY DIFFRACTIONr_chiral_restr0.0870.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029854
X-RAY DIFFRACTIONr_nbd_refined0.2190.25327
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2493
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.211
X-RAY DIFFRACTIONr_mcbond_it0.3251.57816
X-RAY DIFFRACTIONr_mcangle_it0.501212329
X-RAY DIFFRACTIONr_scbond_it0.86935517
X-RAY DIFFRACTIONr_scangle_it1.4394.54784
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2098tight positional0.050.05
12C2098tight positional0.050.05
13E2098tight positional0.050.05
14G2098tight positional0.060.05
21B783tight positional0.040.05
22D783tight positional0.040.05
23F783tight positional0.050.05
24H783tight positional0.040.05
31M66tight positional0.030.05
32N66tight positional0.040.05
33O66tight positional0.040.05
34P66tight positional0.040.05
11A2098tight thermal0.080.5
12C2098tight thermal0.070.5
13E2098tight thermal0.080.5
14G2098tight thermal0.080.5
21B783tight thermal0.090.5
22D783tight thermal0.080.5
23F783tight thermal0.090.5
24H783tight thermal0.090.5
31M66tight thermal0.070.5
32N66tight thermal0.070.5
33O66tight thermal0.070.5
34P66tight thermal0.060.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 158 -
Rwork0.337 2691 -
obs--84.57 %
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)
13.1169-0.84160.80315.8741-2.14223.946-0.1624-0.0150.54190.1249-0.0401-0.45-0.1573-0.04090.2024-0.17210.0026-0.1087-0.14-0.02810.067-8.1964-19.4954-11.2699
215.05142.0974-1.68812.3205-0.66611.6596-0.0244-0.10090.93420.140.04590.3027-0.24070.0194-0.0215-0.07960.014-0.0856-0.22130.002-0.0081-45.7035-29.4924-17.517
34.66593.37081.79157.15562.79121.9004-0.1992-0.092-0.2499-0.13280.1583-0.0450.13060.12640.0409-0.10460.05070.0428-0.0840.0667-0.182-26.3251-41.588-14.9602
43.72520.8925-1.07375.5918-2.56393.5406-0.15530.1102-0.7559-0.194-0.0005-0.28260.23290.03840.1558-0.12170.04140.0108-0.1487-0.06770.193-11.47593.454127.7958
512.9852-3.25881.27043.6848-0.37610.62890.03060.2009-0.3869-0.1029-0.02640.35840.25960.0689-0.0043-0.0802-0.04380.0313-0.2041-0.0373-0.0705-48.86813.365334.6659
64.6954-2.3207-2.13875.11761.98632.6159-0.07130.01330.40870.1050.099-0.1753-0.12420.2589-0.0277-0.1046-0.0212-0.0955-0.13490.02620.0358-29.513825.431232.3845
72.989-0.91540.11917.31964.21725.26830.17030.11170.0238-0.6181-0.47280.4268-0.4362-0.30260.3025-0.10330.1035-0.1051-0.09520.0088-0.191812.0084-20.809127.8382
812.6854-1.4787-2.03532.29631.1671.78670.01680.30520.5629-0.15890.1022-0.3361-0.12140.1876-0.1191-0.1415-0.0246-0.0471-0.17080.025-0.196849.4625-30.950434.6846
94.9889-2.65212.84345.1713-1.96853.38170.05550.1302-0.4521-0.16870.08430.25010.1432-0.1506-0.1398-0.1513-0.01870.0418-0.1917-0.011-0.260330.077-43.021632.0326
103.6267-0.0396-0.60075.7223.30885.33490.0354-0.0457-0.90770.4117-0.38160.51680.3464-0.43330.3463-0.143-0.15880.0885-0.0489-0.00470.258515.41694.8594-10.2746
1112.45611.30511.6483.46250.98681.97850.0561-0.2856-0.37830.07550.0569-0.58150.21240.1994-0.113-0.14050.05180.0456-0.17840.0408-0.144552.586614.8444-17.555
124.89942.2001-1.73293.5463-2.20213.38020.1208-0.13440.22520.1810.01270.264-0.1924-0.1431-0.1335-0.13990.0353-0.0052-0.21860.0076-0.19933.363626.935-14.7919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 179
2X-RAY DIFFRACTION1M1 - 8
3X-RAY DIFFRACTION2A183 - 277
4X-RAY DIFFRACTION3B2 - 99
5X-RAY DIFFRACTION4C1 - 179
6X-RAY DIFFRACTION4O1 - 8
7X-RAY DIFFRACTION5C183 - 277
8X-RAY DIFFRACTION6D2 - 99
9X-RAY DIFFRACTION7E1 - 179
10X-RAY DIFFRACTION7N1 - 8
11X-RAY DIFFRACTION8E183 - 277
12X-RAY DIFFRACTION9F2 - 99
13X-RAY DIFFRACTION10G1 - 179
14X-RAY DIFFRACTION10P1 - 8
15X-RAY DIFFRACTION11G183 - 277
16X-RAY DIFFRACTION12H2 - 99

+
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