[English] 日本語
Yorodumi
- PDB-4bh6: Insights into degron recognition by APC coactivators from the str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bh6
TitleInsights into degron recognition by APC coactivators from the structure of an Acm1-Cdh1 complex
Components
  • APC/C ACTIVATOR PROTEIN CDH1
  • APC/C-CDH1 MODULATOR 1
KeywordsCELL CYCLE / ANAPHASE PROMOTING COMPLEX / ACM1 / UBIQUITINATION / D BOX
Function / homology
Function and homology information


negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / ubiquitin-protein transferase inhibitor activity / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex binding / ubiquitin ligase activator activity ...negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / ubiquitin-protein transferase inhibitor activity / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex binding / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cyclin binding / positive regulation of protein ubiquitination / positive regulation of protein catabolic process / cell cycle / cell division / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2450 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2450 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Helix non-globular / Special / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
APC/C activator protein CDH1 / APC/C-CDH1 modulator 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHe, J. / Chao, W.C.H. / Zhang, Z. / Yang, J. / Cronin, N. / Barford, D.
CitationJournal: Mol.Cell / Year: 2013
Title: Insights Into Degron Recognition by Apc/C Coactivators from the Structure of an Acm1-Cdh1 Complex.
Authors: He, J. / Chao, W.C. / Zhang, Z. / Yang, J. / Cronin, N. / Barford, D.
History
DepositionMar 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
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_conn
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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APC/C ACTIVATOR PROTEIN CDH1
B: APC/C ACTIVATOR PROTEIN CDH1
C: APC/C ACTIVATOR PROTEIN CDH1
D: APC/C ACTIVATOR PROTEIN CDH1
E: APC/C ACTIVATOR PROTEIN CDH1
F: APC/C ACTIVATOR PROTEIN CDH1
G: APC/C ACTIVATOR PROTEIN CDH1
H: APC/C ACTIVATOR PROTEIN CDH1
I: APC/C-CDH1 MODULATOR 1
J: APC/C-CDH1 MODULATOR 1
K: APC/C-CDH1 MODULATOR 1
L: APC/C-CDH1 MODULATOR 1
M: APC/C-CDH1 MODULATOR 1
N: APC/C-CDH1 MODULATOR 1
O: APC/C-CDH1 MODULATOR 1
P: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)339,30016
Polymers339,30016
Non-polymers00
Water50428
1
D: APC/C ACTIVATOR PROTEIN CDH1
L: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-12.8 kcal/mol
Surface area15450 Å2
MethodPISA
2
H: APC/C ACTIVATOR PROTEIN CDH1
P: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9.1 kcal/mol
Surface area12650 Å2
MethodPISA
3
A: APC/C ACTIVATOR PROTEIN CDH1
I: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-13.4 kcal/mol
Surface area17360 Å2
MethodPISA
4
C: APC/C ACTIVATOR PROTEIN CDH1
K: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-13.5 kcal/mol
Surface area17230 Å2
MethodPISA
5
B: APC/C ACTIVATOR PROTEIN CDH1
J: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-12.5 kcal/mol
Surface area16870 Å2
MethodPISA
6
E: APC/C ACTIVATOR PROTEIN CDH1
N: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11.7 kcal/mol
Surface area15700 Å2
MethodPISA
7
F: APC/C ACTIVATOR PROTEIN CDH1
M: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9.7 kcal/mol
Surface area15950 Å2
MethodPISA
8
G: APC/C ACTIVATOR PROTEIN CDH1
O: APC/C-CDH1 MODULATOR 1


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-11.4 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.431, 188.142, 93.440
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12I
22J
32K
42L
13M
23N
33O
43P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A248 - 546
2111B248 - 546
3111C248 - 546
4111D248 - 546
5111E248 - 546
6111F248 - 546
7111G248 - 546
8111H248 - 546
1121I60 - 111
2121J60 - 111
3121K60 - 111
4121L60 - 111
1131M62 - 79
2131N62 - 70
3131O62 - 79
4131P62 - 79

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998632, 0.013169, 0.050598), (-0.011458, 0.999357, -0.033962), (-0.051013, 0.033336, 0.998141)103.13516, -4.5987, 42.86938
3given(-0.496111, -0.12322, -0.859471), (0.147622, -0.987437, 0.056355), (-0.855618, -0.098919, 0.508068)3.03378, 9.75679, 3.37357
4given(-0.473363, -0.131345, -0.87102), (0.104531, -0.99021, 0.09251), (-0.874643, -0.047258, 0.482458)-86.19245, 25.83005, -61.10667
5given(-0.62529, 0.74494, -0.232545), (-0.778044, -0.61819, 0.111755), (-0.060506, 0.25081, 0.966144)-12.65025, -15.59597, 11.87326
6given(0.563088, -0.698928, 0.440944), (0.29615, 0.6688, 0.68191), (-0.77151, -0.25339, 0.583581)-5.02476, -25.18367, 15.73205
7given(-0.568825, 0.762201, -0.309013), (-0.812253, -0.579612, 0.065527), (-0.129163, 0.28827, 0.948798)-85.48651, -93.51279, 44.11447
8given(0.531323, -0.675022, 0.511899), (0.236734, 0.698479, 0.67534), (-0.81342, -0.23764, 0.530919)72.60971, 31.23273, -39.08913
9given(1), (1), (1)
10given(0.998241, -0.003186, 0.059199), (0.005263, 0.999375, -0.03496), (-0.059051, 0.03521, 0.997634)103.17595, -2.55977, 41.88637
11given(-0.478434, -0.124859, -0.869201), (0.111311, -0.990478, 0.081012), (-0.87104, -0.057993, 0.487777)2.30074, 10.98607, 2.52715
12given(-0.44945, -0.139526, -0.882342), (0.07325, -0.990157, 0.119263), (-0.890297, -0.011028, 0.455247)-84.85048, 24.93556, -64.60947
13given(1), (1), (1)
14given(-0.493656, 0.041288, -0.868677), (-0.070262, -0.9975, -0.007482), (-0.866814, 0.057341, 0.495323)-0.32589, 12.07526, 0.25034
15given(-0.43458, 0.033238, -0.90002), (-0.117133, -0.992917, 0.01989), (-0.892984, 0.114066, 0.435395)-86.61104, 2.85321, -68.25789
16given(0.994951, -0.000963, 0.100359), (0.010256, 0.995695, -0.092126), (-0.099838, 0.09269, 0.990677)104.53623, -5.46042, 37.52433

-
Components

#1: Protein
APC/C ACTIVATOR PROTEIN CDH1 / CDH1 / CDC20 HOMOLOG 1 / HOMOLOG OF CDC TWENTY 1


Mass: 34273.637 Da / Num. of mol.: 8 / Fragment: WD40 DOMAIN, RESIDUES 241-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53197
#2: Protein
APC/C-CDH1 MODULATOR 1


Mass: 8138.838 Da / Num. of mol.: 8 / Fragment: RESIDUES 59-128
Source method: isolated from a genetically manipulated source
Details: PHOSPORYLATED AT SER 102
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q08981
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHOSERINE (SEP): SPONTANEOUSLY PHOSPHORYLATED IN INSECT CELL SYSTEM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6 / Details: PEG, pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→93.4 Å / Num. obs: 72799 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AEZ
Resolution: 2.9→69.27 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.895 / SU B: 42.382 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25725 3671 5 %RANDOM
Rwork0.21882 ---
obs0.22075 69120 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0.18 Å2
2---0.5 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21463 0 0 28 21491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01921932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.92829819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55852734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76924.1381015
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.174153563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43415126
X-RAY DIFFRACTIONr_chiral_restr0.1040.23352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116628
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23028.26
12B23025.98
13C23026.02
14D23025.72
15E23025.17
16F23025.09
17G230211.95
18H23029.39
21I4107.31
22J4106.46
23K4105.87
24L4105.92
31M12035.49
32N12018.01
33O12035.38
34P12088.37
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 270 -
Rwork0.315 5222 -
obs--97.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4707-0.0323-0.17492.62490.50082.1317-0.04150.0481-0.2277-0.1216-0.13320.22320.2447-0.43390.17470.0477-0.0558-0.01350.29-0.10420.1901-29.435-15.027-18.755
21.1234-0.1880.25412.43151.07451.8387-0.1513-0.0647-0.4124-0.013-0.17610.18670.0455-0.37870.32740.06980.0664-0.01450.2737-0.20660.5102-129.069-14.173-67.834
32.16420.12381.08471.8838-0.18751.81660.0269-0.30150.35940.0855-0.0236-0.0461-0.1754-0.2151-0.00330.1856-0.05190.0790.1554-0.04470.119531.45630.69115.171
42.45040.0781.20451.97130.06193.15850.0617-0.23780.40810.244-0.03410.29680.1-0.4497-0.02760.25450.01490.11470.17490.07550.2361-68.13230.991-32.825
53.89940.4421.03780.6930.54874.76440.31710.5575-0.6116-0.01130.1427-0.12680.53950.9306-0.45980.16670.1846-0.08340.3589-0.18210.151811.889-20.408-25.814
63.05540.02151.14272.4783-0.1592.68910.11690.53740.3966-0.593-0.17860.12020.14020.13290.06170.23350.02110.01010.27540.18020.183915.98132.545-23.985
71.8241-0.4406-0.74460.84180.19721.90670.10830.035-0.09590.0611-0.0281-0.3403-0.04280.3964-0.08020.1087-0.0559-0.05770.1966-0.07720.3235-87.581-20.799-71.947
81.76810.75220.18996.5166-3.03936.75540.06990.51720.6121-1.35071.04611.77090.798-1.0375-1.11610.3395-0.2394-0.37270.60740.57370.7172-81.33331.539-72.822
93.08891.42831.23031.09270.7451.0745-0.2460.2152-0.0301-0.14650.02350.04460.01940.1110.22250.2059-0.03350.03170.2124-0.06040.2459-12.866-15.167-27.027
104.44951.54741.39763.65091.33941.7992-0.12280.408-0.3207-0.54910.0747-0.13-0.29930.12340.0480.20670.06140.08030.1513-0.11120.5359-116.466-22.051-77.564
112.23471.01761.32451.90120.92511.28280.09440.17150.4394-0.1012-0.14720.0978-0.1509-0.05870.05270.3095-0.02130.11860.16840.0840.199929.7329.71-3.49
121.8341-0.70020.57711.0733-0.21781.3596-0.03240.24060.166-0.2808-0.0660.26110.1068-0.07250.09850.4646-0.0961-0.01190.25380.19930.3757-69.06329.402-51.202
133.83586.80651.049112.25641.980.3767-1.37971.0888-0.8351-2.89551.5315-1.382-0.5742-0.0512-0.15182.13950.20510.14542.0213-0.14390.503122.25721.959-45.919
1413.51747.8351-2.79095.44570.9878.1018-0.76450.56670.3907-0.84331.14490.0808-0.90142.0216-0.38030.2884-0.15060.1071.909-0.32740.300629.162-12.376-42.358
1512.074310.38910.62638.95170.54350.0461-0.40970.5729-0.7081-0.38710.4877-0.731-0.12090.0251-0.07790.74550.04880.33411.55570.04241.2201-68.581-13.15-87.493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A245 - 548
2X-RAY DIFFRACTION2B245 - 548
3X-RAY DIFFRACTION3C245 - 548
4X-RAY DIFFRACTION4D244 - 548
5X-RAY DIFFRACTION5E246 - 548
6X-RAY DIFFRACTION6F245 - 548
7X-RAY DIFFRACTION7G245 - 547
8X-RAY DIFFRACTION8H248 - 546
9X-RAY DIFFRACTION9I60 - 125
10X-RAY DIFFRACTION10J60 - 125
11X-RAY DIFFRACTION11K60 - 125
12X-RAY DIFFRACTION12L60 - 111
13X-RAY DIFFRACTION13M60 - 80
14X-RAY DIFFRACTION14N60 - 79
15X-RAY DIFFRACTION15O60 - 79

+
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://pdbjlvh1.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