[English] 日本語
Yorodumi
- PDB-3zng: Ankyrin repeat and SOCS-box protein 9 (ASB9) in complex with Elon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zng
TitleAnkyrin repeat and SOCS-box protein 9 (ASB9) in complex with ElonginB and ElonginC
Components
  • ANKYRIN REPEAT AND SOCS BOX PROTEIN 9
  • TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
  • TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
KeywordsTRANSCRIPTION / CULLIN-RING LIGASE
Function / homology
Function and homology information


target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript ...target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / : / SOCS box / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Potassium Channel Kv1.1; Chain A ...Ankyrin repeat and SOCS box protein 9/11, SOCS box domain / : / SOCS box / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Elongin-C / Elongin B / Ankyrin repeat-containing domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongin-C / Elongin-B / Ankyrin repeat and SOCS box protein 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsThomas, J. / Van Molle, I. / Ciulli, A.
CitationJournal: Biochemistry / Year: 2013
Title: Multimeric Complexes Among Ankyrin-Repeat and Socs-Box Protein 9 (Asb9), Elonginbc, and Cullin 5: Insights Into the Structure and Assembly of Ecs-Type Cullin-Ring E3 Ubiquitin Ligases.
Authors: Thomas, J.C. / Matak-Vinkovic, D. / Van Molle, I. / Ciulli, A.
History
DepositionFeb 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references / Source and taxonomy
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANKYRIN REPEAT AND SOCS BOX PROTEIN 9
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
D: ANKYRIN REPEAT AND SOCS BOX PROTEIN 9
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1587
Polymers107,0966
Non-polymers621
Water63135
1
A: ANKYRIN REPEAT AND SOCS BOX PROTEIN 9
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6104
Polymers53,5483
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-45.4 kcal/mol
Surface area20210 Å2
MethodPISA
2
D: ANKYRIN REPEAT AND SOCS BOX PROTEIN 9
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2


Theoretical massNumber of molelcules
Total (without water)53,5483
Polymers53,5483
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-43.4 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.110, 103.130, 109.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein ANKYRIN REPEAT AND SOCS BOX PROTEIN 9 / ASB-9 / ASB9


Mass: 29425.727 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96DX5
#2: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 / ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / ...ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15 / ELONGINC


Mass: 10974.616 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#3: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / ...ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18 / ELONGINB


Mass: 13147.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 34-294 ONLY. SEQUENCE CONTAINS ADDITIONAL RESIDUES AENLYFQ AT C-TERMINUS LEFT OVER FROM ...RESIDUES 34-294 ONLY. SEQUENCE CONTAINS ADDITIONAL RESIDUES AENLYFQ AT C-TERMINUS LEFT OVER FROM CLEAVAGE OF HIS6 AND FLAG TAGS RESIDUES 17-112 ONLY. SEQUENCE CONTAINS ADDITIONAL M RESIDUE AT N-TERMINUS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PROPANE, PH 6.7, 0.2 M SODIUM MALONATE, 22% PEG 3350, 10% ETHYLENE GLYCOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97879
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.85→50.64 Å / Num. obs: 30887 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 11.4 % / Biso Wilson estimate: 72.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.2
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKJ

3zkj


Resolution: 2.85→50.638 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 26.14 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2416 1549 5.1 %
Rwork0.1946 --
obs0.1969 30665 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→50.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 4 35 6507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096634
X-RAY DIFFRACTIONf_angle_d1.1859026
X-RAY DIFFRACTIONf_dihedral_angle_d14.0342374
X-RAY DIFFRACTIONf_chiral_restr0.0631045
X-RAY DIFFRACTIONf_plane_restr0.0081173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.94210.32381260.30732580X-RAY DIFFRACTION98
2.9421-3.04720.41051150.28032628X-RAY DIFFRACTION98
3.0472-3.16920.35061440.27732575X-RAY DIFFRACTION99
3.1692-3.31340.29041400.2532589X-RAY DIFFRACTION99
3.3134-3.48810.27161510.21522617X-RAY DIFFRACTION99
3.4881-3.70660.25961420.19642630X-RAY DIFFRACTION99
3.7066-3.99260.27811300.17812645X-RAY DIFFRACTION100
3.9926-4.39420.20841500.15722664X-RAY DIFFRACTION99
4.3942-5.02960.19661480.15112646X-RAY DIFFRACTION100
5.0296-6.33480.23821510.19482713X-RAY DIFFRACTION100
6.3348-50.64570.20071520.18832829X-RAY DIFFRACTION99
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)
12.833-0.72322.15832.8498-0.58485.00580.0171-0.1620.0195-0.0496-0.2570.5296-0.0642-0.24980.20320.3648-0.0497-0.13550.4521-0.00280.7096-53.44122.2767-9.0556
24.1702-0.88652.48982.07710.19851.7687-0.0937-0.23670.03330.0692-0.2335-0.0128-0.42030.44140.18750.384-0.0858-0.07550.5020.04970.6359-44.221921.21592.8723
32.9652-2.22312.08315.7905-1.32073.3733-0.0456-0.2047-0.2780.35820.10310.58520.2738-0.3036-0.04620.457-0.05280.09130.38310.06320.5165-35.206110.61913.7568
44.73790.9670.57794.62711.03562.0283-0.4055-0.2795-0.47980.07020.2309-0.02860.5343-0.34170.15490.5437-0.03360.13870.40790.04710.3697-22.607311.698921.5695
54.7391.68191.53030.811.64416.2518-0.0879-1.32180.18590.4904-0.4113-0.54760.38840.20930.58190.69950.1115-0.24340.73050.13930.9099-0.497214.868539.3285
67.786-8.3303-0.42189.6062-0.70252.0219-0.49040.0082-0.27650.26690.16360.29160.5420.6611-0.08850.6090.00380.11810.67580.16220.68061.50649.447229.074
74.3714-3.68270.41074.4369-1.6641.36130.1861-0.40960.29670.6111-0.0336-1.52480.29941.24280.26090.65450.0721-0.38580.94660.04250.88873.368819.000933.2326
84.11041.0888-0.91512.246-2.1874.3109-0.2023-0.9213-0.82590.39650.06680.0762-0.4864-0.11160.06280.57740.1166-0.10010.60780.21460.7095-10.180514.508236.2605
93.9814-0.60280.840.2826-0.09280.6252-0.4348-0.746-1.99910.86350.62731.3510.0554-0.6065-0.44460.8170.16320.19420.78730.43061.0041-20.1468.516135.9816
109.7784-2.93050.82698.0804-2.766810.0033-0.49610.2258-0.60550.7166-0.0671-0.7107-0.41240.2360.27610.34580.0286-0.05150.42580.04160.5241-9.524919.826726.9593
113.26040.32331.99322.35411.46632.2335-0.4145-0.4382-0.40251.36760.45810.3514-0.2129-1.0761-0.31511.30920.4767-0.31871.07820.18640.5608-7.869914.461949.3557
122.5856-1.08580.52843.0505-1.1991.338-0.3743-0.9583-0.46630.619-0.0299-0.62160.70671.01810.26381.91280.6971-0.57361.11740.11180.5543-1.935110.384256.5866
133.1767-0.95952.26881.5141-1.29452.81620.1048-0.1293-0.29160.7498-0.0732-0.42930.65591.39041.12891.43770.0596-0.38381.56970.87380.18651.123915.341659.1659
140.3827-0.7432-0.45871.4951.36245.0747-0.4814-0.8345-0.0970.7932-0.90940.7110.3177-0.20040.09721.1260.26590.0571.38430.15990.6461-16.167816.195150.1331
153.61520.45771.75813.26450.22725.7072-0.2395-0.37150.20270.47770.4046-0.4175-1.4253-0.33260.1510.89140.0762-0.11860.6864-0.12250.8192-14.618831.300331.5691
163.8846-3.1371-2.00266.1339-3.55618.47260.00040.1416-1.4368-0.1734-0.04050.89190.4648-1.34990.27350.47390.006-0.23990.5345-0.15180.8093-24.1475-12.08975.7633
173.2120.49851.33212.7134-0.63025.60520.06630.199-0.1352-0.03510.0417-0.21580.0270.1345-0.17680.51320.0726-0.07970.3933-0.04050.5554-19.1143-5.3774-3.3019
184.3749-0.90270.75844.152-1.2161.4922-0.03980.2612-0.1879-0.4122-0.0050.33420.05630.18860.05490.69710.0688-0.07770.7253-0.07730.4495-32.85429.0614-23.2093
192.41320.5181-1.23751.8392-1.53481.5890.2535-0.0310.0195-0.3104-0.0492-0.0866-0.2991-0.0356-0.1850.85470.02170.01450.7566-0.11490.4075-30.072523.3788-28.8212
201.9777-0.80220.96722.3012-1.05192.29180.7492-0.44270.4164-1.0153-0.5406-0.6236-1.0829-0.3021-0.25091.69630.0780.14170.8654-0.17970.5242-28.533639.2129-51.6363
213.5357-0.7988-0.29613.01050.19790.0686-0.0122-0.67170.04470.03840.1835-0.3815-1.2884-0.6639-0.04481.47830.04140.12910.871-0.16630.3868-28.526735.7977-45.5463
223.0899-1.3529-2.88782.7289-0.0194.36530.28660.2584-0.0122-0.2021-0.11170.3495-0.4288-1.73950.24641.0764-0.00930.08671.4977-0.33990.3407-33.311420.6914-44.9037
233.4312-2.0012.22127.5785-2.25584.0239-0.6522-0.1062-0.10910.60040.03690.1815-0.9344-0.13130.59181.3669-0.10340.15750.8645-0.16990.5575-23.351433.1858-36.9103
246.70846.147-1.25899.6456-1.30383.81110.9508-0.64060.43351.0693-0.47360.1352-1.4325-1.0642-0.28751.10390.17420.07010.8582-0.1070.4509-25.536629.4394-58.9916
251.6685-0.98421.29233.45592.0253.7525-0.2712-0.6250.637-0.20340.5830.0897-0.927-0.9294-0.2151.59230.12780.09150.67760.00350.4383-24.339634.6327-57.9076
263.40420.4365-0.90913.61930.46921.57310.49840.84730.0573-0.4815-0.44790.1916-1.7298-2.1486-0.07671.38010.42510.06010.9778-0.08880.4963-27.42133.3007-69.5772
272.00823.00570.65419.09240.08076.40910.2902-0.7950.3490.4753-0.0138-0.7241-0.46050.4263-0.44410.64060.01190.09160.8849-0.220.5938-19.56324.4121-70.3637
284.2278-1.69590.23841.62650.97811.23620.2247-0.0118-0.48850.1975-0.68920.23530.5707-1.0819-0.12030.6624-0.05850.03740.7058-0.05380.3832-27.515118.803-64.3715
297.2452-1.3837-6.272.3301-0.39398.6076-0.0366-1.2867-0.74761.19750.51590.29760.3663-0.4095-0.29130.93770.15650.15851.04230.01730.5861-27.232921.839-53.1564
301.4332-0.179-1.53180.8417-0.54252.29180.5612-0.33270.5116-0.42030.0369-0.2522-0.71550.3650.53171.7628-0.07890.38710.6453-0.20730.1715-20.107832.4518-64.2
311.692.43462.56563.79163.93594.43570.1645-1.22151.0383-1.3873-0.59640.6674-2.68230.66520.87731.85-0.01350.13171.07440.01340.6989-13.522138.6698-71.2663
321.3210.55241.66890.76951.8344.50340.0453-0.07310.4386-0.18990.0305-0.0959-1.62260.2275-0.17911.6241-0.20760.18051.1269-0.18970.3076-13.282134.6019-53.328
333.77291.00780.39065.62891.11183.8195-0.11110.0105-0.08030.04180.14050.3624-0.24771.1898-0.01870.7805-0.06290.02920.9955-0.05620.6758-10.416925.0519-33.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 37 THROUGH 104 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 105 THROUGH 136 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 137 THROUGH 220 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 221 THROUGH 294 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 18 THROUGH 38 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 39 THROUGH 45 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 46 THROUGH 66 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 67 THROUGH 82 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 83 THROUGH 96 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 97 THROUGH 112 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 2 THROUGH 23 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 24 THROUGH 35 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 36 THROUGH 46 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 47 THROUGH 75 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 91 THROUGH 105 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 36 THROUGH 48 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 49 THROUGH 136 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 137 THROUGH 234 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 235 THROUGH 294 )
20X-RAY DIFFRACTION20CHAIN E AND (RESID 18 THROUGH 38 )
21X-RAY DIFFRACTION21CHAIN E AND (RESID 39 THROUGH 83 )
22X-RAY DIFFRACTION22CHAIN E AND (RESID 84 THROUGH 96 )
23X-RAY DIFFRACTION23CHAIN E AND (RESID 97 THROUGH 112 )
24X-RAY DIFFRACTION24CHAIN F AND (RESID 2 THROUGH 9 )
25X-RAY DIFFRACTION25CHAIN F AND (RESID 10 THROUGH 18 )
26X-RAY DIFFRACTION26CHAIN F AND (RESID 19 THROUGH 45 )
27X-RAY DIFFRACTION27CHAIN F AND (RESID 46 THROUGH 55 )
28X-RAY DIFFRACTION28CHAIN F AND (RESID 56 THROUGH 65 )
29X-RAY DIFFRACTION29CHAIN F AND (RESID 66 THROUGH 72 )
30X-RAY DIFFRACTION30CHAIN F AND (RESID 73 THROUGH 79 )
31X-RAY DIFFRACTION31CHAIN F AND (RESID 80 THROUGH 89 )
32X-RAY DIFFRACTION32CHAIN F AND (RESID 90 THROUGH 94 )
33X-RAY DIFFRACTION33CHAIN F AND (RESID 95 THROUGH 106 )

+
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