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- PDB-6cim: Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS comple... -

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Basic information

Entry
Database: PDB / ID: 6cim
TitlePre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+
Components
  • (Intact 23RSS substrate ...) x 2
  • (Nicked 12RSS intermediate ...) x 2
  • (V(D)J recombination-activating protein ...) x 2
  • DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
  • High mobility group protein B1
KeywordsRECOMBINATION/DNA / VDJ recombination / RSS / RAG1/2 / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell activation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell activation / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / DNA recombinase complex / negative regulation of CD4-positive, alpha-beta T cell differentiation / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / double-stranded DNA endonuclease activity / pre-B cell allelic exclusion / positive regulation of interleukin-1 production / positive regulation of organ growth / RAGE receptor binding / Regulation of TLR by endogenous ligand / regulation of behavioral fear response / alphav-beta3 integrin-HMGB1 complex / bubble DNA binding / V(D)J recombination / negative regulation of T cell apoptotic process / Apoptosis induced DNA fragmentation / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / negative regulation of thymocyte apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / supercoiled DNA binding / phosphatidylinositol-3,5-bisphosphate binding / apoptotic cell clearance / dendritic cell chemotaxis / positive regulation of T cell differentiation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / IRAK4 deficiency (TLR2/4) / regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / organ growth / T cell lineage commitment / B cell lineage commitment / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / negative regulation of blood vessel endothelial cell migration / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / protein autoubiquitination / Pyroptosis / positive regulation of autophagy / heterochromatin formation / DNA polymerase binding / four-way junction DNA binding / condensed chromosome / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / activation of innate immune response / transcription repressor complex / phosphatidylinositol binding / B cell differentiation / thymus development / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / visual learning / autophagy / double-strand break repair via nonhomologous end joining / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / ubiquitin protein ligase activity / integrin binding
Similarity search - Function
HMG box A DNA-binding domain, conserved site / Recombination-activating protein 1 zinc-finger domain / HMG box A DNA-binding domain signature. / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding ...HMG box A DNA-binding domain, conserved site / Recombination-activating protein 1 zinc-finger domain / HMG box A DNA-binding domain signature. / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Recombination activating protein 2 / RAG2 PHD domain / V-D-J recombination activating protein 2 / Recombination activating protein 2, PHD domain / Galactose oxidase/kelch, beta-propeller / HMG-box domain / HMG (high mobility group) box / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Kelch-type beta propeller / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DNA / DNA (> 10) / High mobility group protein B1 / V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsChuenchor, W. / Chen, X. / Kim, M.S. / Gellert, M. / Yang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036147, DK036144, DK036167 United States
National Institutes of Health/Office of the Director United States
CitationJournal: Mol Cell / Year: 2018
Title: Cracking the DNA Code for V(D)J Recombination.
Authors: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang /
Abstract: To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have ...To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.
History
DepositionFeb 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 1
B: V(D)J recombination-activating protein 2
C: V(D)J recombination-activating protein 1
D: V(D)J recombination-activating protein 2
N: High mobility group protein B1
F: Nicked 12RSS intermediate reverse strand
I: DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
L: Nicked 12RSS intermediate forward strand
G: Intact 23RSS substrate reverse strand
J: Intact 23RSS substrate forward strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,73414
Polymers301,49310
Non-polymers2414
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The assembly was made by mixing of RAG1/2, 12RSS, 23RSS, and HMGB1 in 1:1.2:1.2:2 molar ratio. The tetrameric unit was then purified by gel filtration. The molecular weight ...Evidence: gel filtration, The assembly was made by mixing of RAG1/2, 12RSS, 23RSS, and HMGB1 in 1:1.2:1.2:2 molar ratio. The tetrameric unit was then purified by gel filtration. The molecular weight marker for gel filtration was used to determine the size of the complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31650 Å2
ΔGint-205 kcal/mol
Surface area109700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.678, 123.562, 186.286
Angle α, β, γ (deg.)90.000, 105.600, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 46 or resid 48...
21(chain D and (resid 2 through 37 or (resid 38...
12(chain F and resid 22 through 28) or (chain L and resid 19 through 25)
22(chain G and resid 33 through 39) or (chain J and resid 19 through 25)
13(chain A and ((resid 404 through 410 and (name N...
23(chain C and ((resid 404 through 410 and (name N...
14(chain A and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 2)
24(chain C and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 1)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPHEPHE(chain B and (resid 2 through 46 or resid 48...BB2 - 462 - 46
121PHEPHEILEILE(chain B and (resid 2 through 46 or resid 48...BB48 - 5048 - 50
131GLNGLNLEULEU(chain B and (resid 2 through 46 or resid 48...BB52 - 5752 - 57
141PROPROASNASN(chain B and (resid 2 through 46 or resid 48...BB59 - 11759 - 117
151LYSLYSLYSLYS(chain B and (resid 2 through 46 or resid 48...BB118 - 119118 - 119
161METMETCYSCYS(chain B and (resid 2 through 46 or resid 48...BB1 - 3501 - 350
171METMETCYSCYS(chain B and (resid 2 through 46 or resid 48...BB1 - 3501 - 350
181METMETCYSCYS(chain B and (resid 2 through 46 or resid 48...BB1 - 3501 - 350
191METMETCYSCYS(chain B and (resid 2 through 46 or resid 48...BB1 - 3501 - 350
211SERSERPROPRO(chain D and (resid 2 through 37 or (resid 38...DD2 - 372 - 37
221LYSLYSLYSLYS(chain D and (resid 2 through 37 or (resid 38...DD3838
231METMETSERSER(chain D and (resid 2 through 37 or (resid 38...DD1 - 3511 - 351
241METMETSERSER(chain D and (resid 2 through 37 or (resid 38...DD1 - 3511 - 351
251METMETSERSER(chain D and (resid 2 through 37 or (resid 38...DD1 - 3511 - 351
261METMETSERSER(chain D and (resid 2 through 37 or (resid 38...DD1 - 3511 - 351
112DADADGDG(chain F and resid 22 through 28) or (chain L and resid 19 through 25)FF22 - 2822 - 28
122DCDCDTDT(chain F and resid 22 through 28) or (chain L and resid 19 through 25)LH19 - 253 - 9
212DADADGDG(chain G and resid 33 through 39) or (chain J and resid 19 through 25)GI33 - 3933 - 39
222DCDCDTDT(chain G and resid 33 through 39) or (chain J and resid 19 through 25)JJ19 - 2518 - 24
113GLNGLNGLUGLU(chain A and ((resid 404 through 410 and (name N...AA404 - 41021 - 27
123HISHISASNASN(chain A and ((resid 404 through 410 and (name N...AA395 - 100712 - 624
133HISHISASNASN(chain A and ((resid 404 through 410 and (name N...AA395 - 100712 - 624
143HISHISASNASN(chain A and ((resid 404 through 410 and (name N...AA395 - 100712 - 624
153HISHISASNASN(chain A and ((resid 404 through 410 and (name N...AA395 - 100712 - 624
213GLNGLNGLUGLU(chain C and ((resid 404 through 410 and (name N...CC404 - 41021 - 27
223LEULEUASNASN(chain C and ((resid 404 through 410 and (name N...CC396 - 100713 - 624
233LEULEUASNASN(chain C and ((resid 404 through 410 and (name N...CC396 - 100713 - 624
243LEULEUASNASN(chain C and ((resid 404 through 410 and (name N...CC396 - 100713 - 624
253LEULEUASNASN(chain C and ((resid 404 through 410 and (name N...CC396 - 100713 - 624
114GLUGLUVALVAL(chain A and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 2)AA709 - 742326 - 359
124ILEILEASPASP(chain A and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 2)AA932 - 950549 - 567
214GLUGLUVALVAL(chain C and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 1)CC709 - 742326 - 359
224ILEILEASPASP(chain C and (resid 709 through 742 or resid 932 through 950)) or (chain Z and resid 1)CC932 - 950549 - 567

NCS ensembles :
ID
1
2
3
4

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Components

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V(D)J recombination-activating protein ... , 2 types, 4 molecules ACBD

#1: Protein V(D)J recombination-activating protein 1 / RAG-1


Mass: 71716.141 Da / Num. of mol.: 2 / Mutation: E962Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1 / Plasmid: pLEXm / Details (production host): His(6)-MBP-PreScission / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P15919, Hydrolases; Acting on ester bonds, RING-type E3 ubiquitin transferase
#2: Protein V(D)J recombination-activating protein 2 / RAG-2


Mass: 40036.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Plasmid: pLEXm / Details (production host): His(6)-MBP-PreScission / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P21784

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Nicked 12RSS intermediate ... , 2 types, 2 molecules FL

#4: DNA chain Nicked 12RSS intermediate reverse strand


Mass: 12429.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain Nicked 12RSS intermediate forward strand


Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Intact 23RSS substrate ... , 2 types, 2 molecules GJ

#7: DNA chain Intact 23RSS substrate reverse strand


Mass: 17259.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#8: DNA chain Intact 23RSS substrate forward strand


Mass: 17251.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / DNA chain , 2 types, 2 molecules NI

#3: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 18897.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: H / Gene: HMGB1, HMG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09429
#5: DNA chain DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')


Mass: 3010.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 7 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 39753 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 119.31 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.072 / Rrim(I) all: 0.139 / Χ2: 1.082 / Net I/σ(I): 14.6
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1956 / CC1/2: 0.574 / Rpim(I) all: 0.593 / Rrim(I) all: 1.164 / Χ2: 0.632 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CIK

6cik


Resolution: 3.6→38.693 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.2
RfactorNum. reflection% reflection
Rfree0.2537 2049 5.16 %
Rwork0.214 --
obs0.216 39678 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 283.26 Å2 / Biso mean: 125.2791 Å2 / Biso min: 53.25 Å2
Refinement stepCycle: final / Resolution: 3.6→38.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15215 3565 4 3 18787
Biso mean--87.58 87.9 -
Num. residues----2156
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2886X-RAY DIFFRACTION10.635TORSIONAL
12D2886X-RAY DIFFRACTION10.635TORSIONAL
21F1641X-RAY DIFFRACTION10.635TORSIONAL
22G1641X-RAY DIFFRACTION10.635TORSIONAL
31A488X-RAY DIFFRACTION10.635TORSIONAL
32C488X-RAY DIFFRACTION10.635TORSIONAL
41A268X-RAY DIFFRACTION10.635TORSIONAL
42C268X-RAY DIFFRACTION10.635TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6001-3.68370.34911480.30252403255196
3.6837-3.77580.30211300.268324782608100
3.7758-3.87780.31021370.244125242661100
3.8778-3.99180.25491280.231725382666100
3.9918-4.12050.27461560.212424782634100
4.1205-4.26760.25831450.196724882633100
4.2676-4.43820.22961380.190224822620100
4.4382-4.63990.2521440.188824892633100
4.6399-4.88410.24591420.184725262668100
4.8841-5.18940.2521370.189125292666100
5.1894-5.5890.29571220.213225322654100
5.589-6.14940.25591440.227224952639100
6.1494-7.03460.2471170.228225462663100
7.0346-8.84540.22991280.214425562684100
8.8454-38.69570.23171330.21072565269899

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