[English] 日本語
Yorodumi
- PDB-7ow4: Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ow4
TitleCrystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK)
Components
  • Beta-2-microglobulin
  • KRAS G12D peptide (VVVGADGVGK)
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA / KRAS
Function / homology
Function and homology information


myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / tertiary granule membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling ...myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / tertiary granule membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / VEGFR2 mediated cell proliferation / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to iron(III) ion / Signaling by high-kinase activity BRAF mutants / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Constitutive Signaling by EGFRvIII / negative regulation of forebrain neuron differentiation / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / Signaling by ERBB2 KD Mutants / MHC class I peptide loading complex / Signaling by SCF-KIT / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / Regulation of RAS by GAPs / positive regulation of T cell mediated cytotoxicity / specific granule lumen / RAS processing / recycling endosome membrane / Negative regulation of MAPK pathway
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / : / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains / Small GTPase / Ras family ...Small GTPase, Ras-type / small GTPase Ras family profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / : / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains / Small GTPase / Ras family / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rab subfamily of small GTPases / 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 / : / Small GTP-binding protein domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / GTPase NRas / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsColes, C.H. / Karuppiah, V. / Robinson, R.A.
CitationJournal: Nat Commun / Year: 2022
Title: Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen
Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / ...Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / Aleksic, M. / Lin, A.B. / Robinson, R. / Dukes, J.D. / Liddy, N. / Van der Kamp, M. / Plowman, G.D. / Vuidepot, A. / Cole, D.K. / Whale, A.D. / Chillakuri, C.
History
DepositionJun 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: KRAS G12D peptide (VVVGADGVGK)
D: MHC class I antigen
E: Beta-2-microglobulin
F: KRAS G12D peptide (VVVGADGVGK)
G: MHC class I antigen
H: Beta-2-microglobulin
I: KRAS G12D peptide (VVVGADGVGK)
J: MHC class I antigen
K: Beta-2-microglobulin
L: KRAS G12D peptide (VVVGADGVGK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,41117
Polymers178,93012
Non-polymers4805
Water18,1771009
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: KRAS G12D peptide (VVVGADGVGK)


Theoretical massNumber of molelcules
Total (without water)44,7333
Polymers44,7333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-19 kcal/mol
Surface area19010 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: KRAS G12D peptide (VVVGADGVGK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8294
Polymers44,7333
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-39 kcal/mol
Surface area19250 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: KRAS G12D peptide (VVVGADGVGK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9255
Polymers44,7333
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-30 kcal/mol
Surface area19050 Å2
MethodPISA
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: KRAS G12D peptide (VVVGADGVGK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9255
Polymers44,7333
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-40 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.224, 121.432, 127.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14B
24E
15B
25H
16B
26K
17D
27G
18D
28J
19E
29H
110E
210K
111G
211J
112H
212K

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12GLYGLYARGARGAA1 - 2731 - 273
22GLYGLYARGARGGG1 - 2731 - 273
13GLYGLYARGARGAA1 - 2731 - 273
23GLYGLYARGARGJJ1 - 2731 - 273
14METMETMETMETBB0 - 991 - 100
24METMETMETMETEE0 - 991 - 100
15METMETMETMETBB0 - 991 - 100
25METMETMETMETHH0 - 991 - 100
16METMETMETMETBB0 - 991 - 100
26METMETMETMETKK0 - 991 - 100
17GLYGLYARGARGDD1 - 2731 - 273
27GLYGLYARGARGGG1 - 2731 - 273
18GLYGLYARGARGDD1 - 2731 - 273
28GLYGLYARGARGJJ1 - 2731 - 273
19METMETMETMETEE0 - 991 - 100
29METMETMETMETHH0 - 991 - 100
110METMETMETMETEE0 - 991 - 100
210METMETMETMETKK0 - 991 - 100
111GLYGLYTRPTRPGG1 - 2741 - 274
211GLYGLYTRPTRPJJ1 - 2741 - 274
112METMETMETMETHH0 - 991 - 100
212METMETMETMETKK0 - 991 - 100

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
MHC class I antigen


Mass: 31952.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A583ZB34
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide
KRAS G12D peptide (VVVGADGVGK) / Transforming protein N-Ras / GTPase NRas


Mass: 901.039 Da / Num. of mol.: 4 / Mutation: G12D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01111, small monomeric GTPase
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.81→88.05 Å / Num. obs: 166212 / % possible obs: 100 % / Redundancy: 15.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.069 / Rrim(I) all: 0.269 / Net I/σ(I): 8.7
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 14.5 % / Rmerge(I) obs: 4.611 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 8252 / CC1/2: 0.322 / Rpim(I) all: 1.244 / Rrim(I) all: 4.778 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HN7

2hn7


Resolution: 1.81→88.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.911 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24917 8118 4.9 %RANDOM
Rwork0.21968 ---
obs0.22111 158094 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2---0.73 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.81→88.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 25 1009 13556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312924
X-RAY DIFFRACTIONr_bond_other_d0.0010.01811537
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.65817541
X-RAY DIFFRACTIONr_angle_other_deg1.3061.58826568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83251526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67221.453826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.468152111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.27715120
X-RAY DIFFRACTIONr_chiral_restr0.0670.21585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023226
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7491.366125
X-RAY DIFFRACTIONr_mcbond_other0.7491.366124
X-RAY DIFFRACTIONr_mcangle_it1.2742.0367632
X-RAY DIFFRACTIONr_mcangle_other1.2742.0367633
X-RAY DIFFRACTIONr_scbond_it1.0581.5126799
X-RAY DIFFRACTIONr_scbond_other1.0411.4976779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7122.1919875
X-RAY DIFFRACTIONr_long_range_B_refined4.52816.01314258
X-RAY DIFFRACTIONr_long_range_B_other4.42415.63514089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91120.07
12D91120.07
21A87550.1
22G87550.1
31A87750.09
32J87750.09
41B31280.06
42E31280.06
51B31110.08
52H31110.08
61B30980.08
62K30980.08
71D87570.09
72G87570.09
81D87420.09
82J87420.09
91E31390.09
92H31390.09
101E31360.1
102K31360.1
111G89410.07
112J89410.07
121H31200.08
122K31200.08
LS refinement shellResolution: 1.81→1.856 Å
RfactorNum. reflection% reflection
Rfree0.373 586 -
Rwork0.362 11595 -
obs--99.89 %
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)
11.1522-0.44050.15771.7521-0.5661.12940.09840.19080.1185-0.1556-0.12270.11320.0282-0.08760.02440.02830.00960.01550.0687-0.01380.101227.16114.05419.116
23.3761-1.21680.62541.71290.26221.86030.0247-0.1530.2720.1303-0.0283-0.13850.04150.16820.00360.0471-0.02250.04040.049-0.0260.11240.91819.02931.656
32.4739-3.47721.98574.903-2.78691.60510.410.5160.331-0.541-0.7101-0.38270.2560.38590.30020.28420.14840.06710.28530.06910.542519.69226.577.208
40.8769-0.2143-0.12721.51050.54741.30020.0450.0715-0.0924-0.0723-0.0571-0.1088-0.04180.13230.01210.0142-0.0115-0.0210.05330.03680.072431.27875.69619.85
54.1603-1.1536-0.94031.6072-0.06342.08360.0304-0.1695-0.18810.163-0.02520.1326-0.0571-0.1341-0.00520.0494-0.0291-0.0330.04490.03670.082417.44171.09932.465
60.29180.3932-0.64091.1954-1.88282.9688-0.06460.2002-0.3433-0.3096-0.312-0.26680.47840.33390.37660.22570.2248-0.13810.5355-0.37180.475338.70362.9958.263
71.1759-0.0964-0.15811.6477-0.17270.66990.06730.036-0.0485-0.09890.01630.0688-0.0079-0.0033-0.08360.0418-0.0264-0.00460.0397-0.03040.06873.93727.09246.564
81.4515-0.26820.08555.06370.75761.08480.01090.13910.1030.00390.0293-0.1577-0.14390.0757-0.04020.0356-0.03140.01140.0596-0.00130.040414.74143.04745.563
910.1779-9.0187-5.52378.11124.86983.0063-0.5934-0.1688-0.14840.69050.3799-0.02760.3620.06290.21350.20850.0692-0.0790.2738-0.13320.32368.80912.54756.726
101.2227-0.0916-0.04671.58530.32780.69480.1003-0.01450.0686-0.05340.0379-0.0971-0.0640.0285-0.13810.0553-0.03260.01570.04270.02750.081655.14662.7347.008
111.4044-0.4134-0.05294.9034-0.3850.79860.02840.1621-0.08450.04640.01920.1170.0903-0.0457-0.04760.0195-0.0083-0.01030.05660.00870.032543.83347.07445.606
125.1257-7.12471.003110.9366-1.03080.3257-0.6962-0.41370.36050.83030.5744-0.3388-0.2016-0.09670.12180.25540.07070.07050.24570.05220.225150.58477.30857.655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D1 - 276
5X-RAY DIFFRACTION5E0 - 99
6X-RAY DIFFRACTION6F1 - 10
7X-RAY DIFFRACTION7G1 - 274
8X-RAY DIFFRACTION8H0 - 99
9X-RAY DIFFRACTION9I1 - 10
10X-RAY DIFFRACTION10J1 - 274
11X-RAY DIFFRACTION11K0 - 99
12X-RAY DIFFRACTION12L1 - 10

+
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://pdbjlc1.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