[English] 日本語
Yorodumi
- PDB-6byh: Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6byh
TitleUbiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex.
Components
  • Lysine-specific demethylase 2A
  • Polyubiquitin-B
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING / Ubiquitination
Function / homology
Function and homology information


[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / F-box domain binding / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / F-box domain binding / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / female gonad development / seminiferous tubule development / Prolactin receptor signaling / male meiosis I / cullin family protein binding / histone demethylase activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / molecular function activator activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / regulation of mitochondrial membrane potential / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins
Similarity search - Function
PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type ...PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / S-phase kinase-associated protein 1 / Lysine-specific demethylase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsManczyk, N. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 143277 Canada
CitationJournal: Structure / Year: 2018
Title: A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
Authors: Gorelik, M. / Manczyk, N. / Pavlenco, A. / Kurinov, I. / Sidhu, S.S. / Sicheri, F.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-phase kinase-associated protein 1
B: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2A
F: Lysine-specific demethylase 2A
G: S-phase kinase-associated protein 1
I: Lysine-specific demethylase 2A
C: Polyubiquitin-B
D: Polyubiquitin-B
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)104,2399
Polymers104,2399
Non-polymers00
Water1,26170
1
A: S-phase kinase-associated protein 1
E: Lysine-specific demethylase 2A
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)34,7463
Polymers34,7463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-phase kinase-associated protein 1
F: Lysine-specific demethylase 2A
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)34,7463
Polymers34,7463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: S-phase kinase-associated protein 1
I: Lysine-specific demethylase 2A
C: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)34,7463
Polymers34,7463
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.560, 118.188, 146.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18808.096 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208
#2: Protein/peptide Lysine-specific demethylase 2A / CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F- ...CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F-box protein Lilina / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 5952.017 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2K7, [histone H3]-dimethyl-L-lysine36 demethylase
#3: Protein Polyubiquitin-B


Mass: 9986.385 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 32211 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rsym value: 0.102 / Net I/σ(I): 24.7
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2735 / Rsym value: 1 / % possible all: 85.4

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 5JH5, 5IBK

1ubq

5jh5

5ibk


Resolution: 2.61→45.09 Å / SU ML: 0.39 / σ(F): 1.33 / Phase error: 34.97
RfactorNum. reflection% reflection
Rfree0.294 1640 5.19 %
Rwork0.235 --
obs0.238 31608 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.61→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6165 0 0 70 6235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076274
X-RAY DIFFRACTIONf_angle_d0.8598521
X-RAY DIFFRACTIONf_dihedral_angle_d8.2133793
X-RAY DIFFRACTIONf_chiral_restr0.052998
X-RAY DIFFRACTIONf_plane_restr0.0071087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6114-2.68830.36381250.30122079X-RAY DIFFRACTION83
2.6883-2.7750.44241130.30992467X-RAY DIFFRACTION96
2.775-2.87420.42071190.33252491X-RAY DIFFRACTION97
2.8742-2.98920.49071300.40692361X-RAY DIFFRACTION94
2.9892-3.12530.47991180.3972468X-RAY DIFFRACTION96
3.1253-3.290.3611500.2782553X-RAY DIFFRACTION100
3.29-3.4960.30921560.24412547X-RAY DIFFRACTION100
3.496-3.76580.2931340.21622579X-RAY DIFFRACTION100
3.7658-4.14460.26211360.22552X-RAY DIFFRACTION99
4.1446-4.74370.27121420.18752519X-RAY DIFFRACTION97
4.7437-5.97440.24121620.20482601X-RAY DIFFRACTION100
5.9744-45.09610.21331550.22751X-RAY DIFFRACTION100
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)
12.55280.63540.396.1353.66052.20620.1098-0.87880.21511.00480.6707-0.85481.26790.9985-0.49690.55880.11650.00270.5427-0.0680.5618-8.4628-64.19343.5737
22.2488-5.4028-0.66132.2282.63572.1915-0.0812-0.3857-0.30431.02490.3685-0.3007-0.003-0.4695-0.35370.60670.02990.02170.52830.12390.5229-12.2351-58.580945.7589
32.0715-8.10047.18052.0579-2.35417.2451-1.0407-0.6535-0.40260.8979-0.0104-0.66440.9115-0.8760.19950.48020.05910.1180.56220.12750.7051-22.2624-62.477645.4504
45.2070.77822.65632.7085-0.0155.9681-0.0364-0.3029-0.05350.26320.05320.321-0.13330.1066-0.03550.26430.05240.0880.40640.05080.3837-12.2528-59.070339.1661
55.9709-4.97995.43528.4795-0.17089.2086-0.4128-0.5691-0.02480.48770.09050.6084-0.4174-0.5674-0.12690.4462-0.01120.04520.37010.12690.5801-18.2165-43.353631.9674
64.7878-0.54623.79765.1518-3.74987.9589-0.31530.15950.7031-0.08710.27520.4009-0.386-0.5138-0.17210.29930.00080.0550.26780.04940.4177-19.2467-52.956528.7583
79.9375-4.91174.64847.54280.4345.9824-0.47850.1927-0.2346-0.28550.0420.10760.53140.25830.32560.5967-0.0510.02220.58060.11750.3313-22.2722-49.2259.5472
80.27171.02610.36174.51760.57551.2497-0.1101-1.0009-0.3339-0.86280.5678-0.16821.4839-1.2215-0.5871.3351-0.292-0.52331.16240.23280.8606-34.4354-50.58282.2096
97.1773-1.0774-1.17065.65850.93297.0134-0.3357-1.02490.42040.67150.22230.10710.0035-0.14060.18380.36080.05680.02660.4093-0.0370.3267-17.1737-14.702435.3126
109.1281-2.2086-7.07962.80391.06267.9072-0.4009-0.6609-0.34550.2474-0.0011-0.38460.23980.57990.36860.4602-0.04430.05360.3090.03660.4519-12.4878-31.638325.6481
113.82310.2892-4.47060.5652-0.22777.6491-0.28390.5402-0.2927-0.22390.0993-0.21520.6493-0.34270.11910.42730.00160.00240.40920.01570.3375-6.2253-24.226310.1772
125.3528-2.47291.62972.20482.03751.3489-0.3843-0.1232-0.1246-0.76070.71650.49430.2361-0.2703-0.2270.6194-0.0546-0.00270.50850.14430.3614-24.9976-57.561821.5808
135.835-4.4790.05471.9697-3.94792.1868-0.74890.57480.1821-0.94480.22681.6131-2.23750.5721-0.06740.8054-0.1111-0.10350.52390.120.4845-31.0234-45.00415.285
143.69182.63295.15733.8969-1.292.18990.349-0.4575-0.9346-0.91680.4011.75810.3305-2.3622-0.83540.8796-0.128-0.16910.97160.30760.7318-33.5477-53.686817.0796
158.2328-1.18681.11715.09362.083.5436-0.13430.110.5776-0.4215-0.4102-0.0201-0.52850.50690.63480.5265-0.09890.01860.5290.03130.3045-5.148-17.49314.3576
162.0453-8.22693.80829.3436-3.06267.3647-0.3215-0.545-1.8693-1.38530.9877-0.1550.8976-0.3064-0.23840.5593-0.11740.16270.41660.04190.79551.4971-30.05149.1624
172.33635.4742-2.0972.0262-0.1642.0984-0.1488-0.0562-0.4367-0.6469-0.34990.0687-0.28220.34770.27340.6408-0.02910.02320.5906-0.03820.3879-0.5214-20.3424.9019
188.89641.72571.47829.6835.79636.68260.7226-0.9931-0.16940.41790.4156-0.67680.47641.3088-0.54120.7694-0.10640.00511.233-0.01570.54847.3175-22.343713.8976
199.84712.6788-5.25012.1907-9.19138.7926-0.16560.6452-0.0717-1.22430.6374-0.8039-1.5561-0.9006-0.03931.0035-0.01990.13460.5879-0.28170.872-16.9222-27.995163.4329
205.59063.38533.54833.27411.19419.0295-0.75390.03821.1535-0.31170.2373-0.3111-0.2902-0.43250.52880.51240.007-0.04680.8693-0.4931.0432-21.1296-32.132167.5427
212.8291-0.19831.31875.90461.68196.28850.43870.3395-0.3111-0.2738-0.19860.3279-1.05490.6716-0.13720.6085-0.25190.22760.9006-0.51650.923-20.3043-29.370574.2302
221.6495-0.0973-1.78076.7646-3.79813.8167-0.36530.4108-0.7809-1.41320.05720.38270.6923-0.35850.240.6590.00270.08170.7872-0.38240.9304-20.8868-45.833364.3526
231.0059-0.4809-0.79735.1386-1.71161.5398-0.36210.2763-0.7785-0.5052-0.2264-0.47480.64560.41990.24040.80660.12450.29870.6846-0.3291.2052-16.8029-53.039567.1125
243.8879-2.11410.36516.5979-0.79172.0439-0.02290.1559-1.10180.22680.30860.27980.16790.62340.34090.62310.0520.10110.5415-0.29281.1261-23.4865-44.807876.3167
250.75631.0615-0.99216.63441.6232.2261-1.06510.8983-0.7950.16570.27780.67061.3093-1.18580.62620.9218-0.09070.32020.6148-0.51431.4165-27.0673-53.604872.3152
264.4925-3.40813.85952.5795-3.45532.02390.90010.2578-1.4532-0.33290.58350.0439-1.3374-1.7607-1.31390.87880.17130.43920.88880.02741.5517-23.8173-63.079485.431
275.49470.76927.16197.10612.51819.6341-0.7939-2.5426-0.3661-1.2286-1.1218-1.0201-0.2643-1.42431.61021.23310.11670.59951.2018-0.03191.0434-23.8635-58.492892.5831
281.87523.32511.45519.9913.04352.504-1.3353-0.4616-2.17310.5181-0.0850.83120.8842-0.23410.65191.1848-0.09130.51480.5712-0.35472.0284-32.1914-53.171381.8592
290.97891.0603-0.81191.7072-2.83967.0569-0.76761.5292-1.5902-0.7462-0.2666-0.29931.2218-0.36230.79790.83780.17231.56861.41780.78262.8789-35.6118-54.957987.0336
304.30523.15591.61365.95361.3667.1917-0.1828-0.0789-0.5472-0.3866-0.02530.68480.0715-0.45960.30680.3691-0.0450.01090.5939-0.29080.8814-37.0573-27.872382.3572
313.46651.3302-0.2942.0968-1.48553.32560.0331-0.2316-0.06720.8651-0.51230.9192-0.1465-1.09650.67190.5576-0.01090.05940.4993-0.17650.769-32.6869-22.307191.159
324.2918-1.463-3.20654.7916-3.03036.19370.2791-0.0278-0.12290.7860.0337-1.044-0.32160.5819-0.21660.7217-0.0943-0.060.46-0.21460.7677-24.7619-25.154385.6566
339.1089-2.7742-0.57385.7586-3.14597.7167-0.03970.1126-0.4168-0.92230.4516-0.651-0.0818-0.2687-0.26130.3628-0.08970.02090.5333-0.18150.6663-28.6959-20.413882.1735
340.3349-0.9396-2.13362.1687-0.13047.3604-0.03650.3346-0.9955-0.1084-0.20230.36260.1105-0.7720.2620.4229-0.08650.02020.52490.0130.8249-30.0958-72.437933.5261
350.97810.3457-2.4742.01552.8415.9729-0.10510.6966-0.69060.4969-0.31691.33510.4677-0.6540.18640.326-0.01530.01840.6305-0.1290.8252-32.1867-75.800835.9588
364.523.02761.53718.9769-2.92756.55450.14480.4612-1.1596-0.60220.0904-0.60920.95610.5203-0.07190.47920.05020.2040.3836-0.07590.7697-22.1399-81.315532.0716
376.08571.05431.14618.4722-1.49326.18430.4009-0.1325-0.56290.2309-0.3929-0.36510.59360.12120.12060.43120.06770.08050.3942-0.00870.5681-21.7088-78.820937.3608
384.38193.07941.79632.0752.3447.0979-0.1857-0.17160.75750.5961-0.4253-0.1108-0.70320.37410.85210.3893-0.0668-0.11630.37950.00840.5668-0.88522.322131.3537
392.74253.13640.22168.4934-3.0987.76730.10310.03010.1585-0.9024-0.2838-1.14430.48280.98110.65760.69760.15310.18660.48960.10160.43430.7245-10.641619.7981
407.52922.05553.08129.8844-2.22678.1486-0.2453-0.1051.08370.5252-0.0421-1.3935-0.63860.42820.34680.28160.02320.02240.42860.07050.3797-0.75376.055829.0877
419.74062.2063-5.50166.35731.21229.76870.53241.17540.1105-0.5956-0.51150.6128-0.643-0.1974-0.37680.40550.0209-0.04320.30210.0430.6372-3.35576.468221.9068
428.00991.9252-6.93354.2184-0.44518.1540.00211.17541.5378-0.11470.22470.6029-0.0861-0.7387-0.1140.3986-0.0294-0.05330.3550.1280.5799-8.33860.522820.9538
438.18763.8279-5.47482.02-2.44163.62180.68090.09281.164-0.2019-0.52661.85620.3924-0.5325-0.14830.44490.0371-0.04090.5197-0.11060.6646-14.21790.893334.5842
447.695-2.02944.04992.018-0.02762.23140.27340.05751.3665-1.0726-0.42681.2461-1.3427-1.48510.39070.55360.0199-0.05690.5712-0.11520.6201-14.99429.466326.8622
458.1992-2.0244-2.66388.27643.73684.84880.3789-0.42870.3438-0.1137-0.53540.3306-0.6567-0.58460.23410.38930.04340.05190.35250.04810.4131-8.5034.943231.4267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 12 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 13 THROUGH 23 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 24 THROUGH 32 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 33 THROUGH 67 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 68 THROUGH 96 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 97 THROUGH 126 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 127 THROUGH 146 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 147 THROUGH 155 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 0 THROUGH 67 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 68 THROUGH 96 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 97 THROUGH 162 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 887 THROUGH 904 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 905 THROUGH 915 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 916 THROUGH 931 )
15X-RAY DIFFRACTION15CHAIN 'F' AND (RESID 887 THROUGH 904 )
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 905 THROUGH 913 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 914 THROUGH 923 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 924 THROUGH 931 )
19X-RAY DIFFRACTION19CHAIN 'G' AND (RESID 0 THROUGH 7 )
20X-RAY DIFFRACTION20CHAIN 'G' AND (RESID 8 THROUGH 32 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 33 THROUGH 51 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 52 THROUGH 86 )
23X-RAY DIFFRACTION23CHAIN 'G' AND (RESID 87 THROUGH 96 )
24X-RAY DIFFRACTION24CHAIN 'G' AND (RESID 97 THROUGH 110 )
25X-RAY DIFFRACTION25CHAIN 'G' AND (RESID 111 THROUGH 131 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 132 THROUGH 139 )
27X-RAY DIFFRACTION27CHAIN 'G' AND (RESID 140 THROUGH 144 )
28X-RAY DIFFRACTION28CHAIN 'I' AND (RESID 889 THROUGH 915 )
29X-RAY DIFFRACTION29CHAIN 'I' AND (RESID 916 THROUGH 927 )
30X-RAY DIFFRACTION30CHAIN 'C' AND (RESID -2 THROUGH 25 )
31X-RAY DIFFRACTION31CHAIN 'C' AND (RESID 26 THROUGH 42 )
32X-RAY DIFFRACTION32CHAIN 'C' AND (RESID 43 THROUGH 62 )
33X-RAY DIFFRACTION33CHAIN 'C' AND (RESID 63 THROUGH 81 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID -1 THROUGH 16 )
35X-RAY DIFFRACTION35CHAIN 'D' AND (RESID 17 THROUGH 25 )
36X-RAY DIFFRACTION36CHAIN 'D' AND (RESID 26 THROUGH 64 )
37X-RAY DIFFRACTION37CHAIN 'D' AND (RESID 65 THROUGH 83 )
38X-RAY DIFFRACTION38CHAIN 'H' AND (RESID -1 THROUGH 9 )
39X-RAY DIFFRACTION39CHAIN 'H' AND (RESID 10 THROUGH 16 )
40X-RAY DIFFRACTION40CHAIN 'H' AND (RESID 17 THROUGH 30 )
41X-RAY DIFFRACTION41CHAIN 'H' AND (RESID 31 THROUGH 42 )
42X-RAY DIFFRACTION42CHAIN 'H' AND (RESID 43 THROUGH 52 )
43X-RAY DIFFRACTION43CHAIN 'H' AND (RESID 53 THROUGH 57 )
44X-RAY DIFFRACTION44CHAIN 'H' AND (RESID 58 THROUGH 62 )
45X-RAY DIFFRACTION45CHAIN 'H' AND (RESID 63 THROUGH 82 )

+
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