[English] 日本語
Yorodumi
- PDB-4mbe: Sac3:Sus1:Cdc31:Nup1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mbe
TitleSac3:Sus1:Cdc31:Nup1 complex
Components
  • Cell division control protein 31
  • Nuclear mRNA export protein SAC3
  • Nucleoporin NUP1
  • Protein SUS1
KeywordsPROTEIN TRANSPORT / TRANSCRIPTION / mRNA nuclear export / mRNA
Function / homology
Function and homology information


half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / : / mitotic spindle pole body / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / Golgi vesicle transport / nuclear pore central transport channel / transcription export complex 2 ...half bridge of spindle pole body / actin filament-based process / spindle pole body duplication / DUBm complex / : / mitotic spindle pole body / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / Golgi vesicle transport / nuclear pore central transport channel / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / SLIK (SAGA-like) complex / nuclear pore nuclear basket / mRNA 3'-end processing / structural constituent of nuclear pore / RNA export from nucleus / SAGA complex / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear localization sequence binding / NLS-bearing protein import into nucleus / enzyme activator activity / ribosomal large subunit export from nucleus / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / nuclear pore / protein export from nucleus / P-body / transcription elongation by RNA polymerase II / ribosomal small subunit biogenesis / protein import into nucleus / regulation of protein localization / protein transport / mitotic cell cycle / nuclear envelope / chromatin organization / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / transcription coactivator activity / molecular adaptor activity / cell division / chromatin binding / calcium ion binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1760 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1760 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Nuclear pore complex protein / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / EF-hand / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division control protein 31 / Nucleoporin NUP1 / Nuclear mRNA export protein SAC3 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.612 Å
AuthorsJani, D. / Meineke, B. / Stewart, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export.
Authors: Jani, D. / Valkov, E. / Stewart, M.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
D: Cell division control protein 31
E: Nuclear mRNA export protein SAC3
F: Protein SUS1
H: Nucleoporin NUP1
G: Nucleoporin NUP1
X: Nucleoporin NUP1
Y: Nucleoporin NUP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,71814
Polymers84,55810
Non-polymers1604
Water59433
1
A: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1
G: Nucleoporin NUP1
X: Nucleoporin NUP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3597
Polymers42,2795
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-93 kcal/mol
Surface area16960 Å2
MethodPISA
2
D: Cell division control protein 31
E: Nuclear mRNA export protein SAC3
F: Protein SUS1
H: Nucleoporin NUP1
Y: Nucleoporin NUP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3597
Polymers42,2795
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-92 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.270, 62.399, 124.601
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain D and segid
12chain B and segid
22chain E and segid
13chain C and segid
23chain F and segid
14chain G and segid G
24chain H and segid H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain D and segidD0
112chain B and segidB0
212chain E and segidE0
113chain C and segidC0
213chain F and segidF0
114chain G and segid GG0
214chain H and segid HH0

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein Cell division control protein 31 / Nuclear pore protein CDC31 / Nucleoporin CDC31


Mass: 18774.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC31, DSK1, YOR257W / Production host: Escherichia coli (E. coli) / References: UniProt: P06704
#2: Protein Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator


Mass: 6623.573 Da / Num. of mol.: 2 / Fragment: CDC31 interacting region, residues 753-805
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SAC3, LEP1, YDR159W, YD8358.13 / Production host: Escherichia coli (E. coli) / References: UniProt: P46674
#3: Protein Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SUS1, YBR111W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WNK7

-
Protein/peptide , 1 types, 4 molecules HGXY

#4: Protein/peptide
Nucleoporin NUP1 / Nuclear pore protein NUP1


Mass: 2893.461 Da / Num. of mol.: 4 / Fragment: FXF 1 repeat containing region, residues 316-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NUP1, YOR098C, YOR3182C / Production host: Escherichia coli (E. coli) / References: UniProt: P20676

-
Non-polymers , 2 types, 37 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.61→43.8 Å / Num. all: 23841 / Num. obs: 23841 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.61→2.73 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FWB

3fwb


Resolution: 2.612→43.8 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1219 5.12 %random
Rwork0.1998 ---
obs0.2017 23815 99.73 %-
all-23815 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.612→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5048 0 4 33 5085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045118
X-RAY DIFFRACTIONf_angle_d0.8316867
X-RAY DIFFRACTIONf_dihedral_angle_d13.9961969
X-RAY DIFFRACTIONf_chiral_restr0.05763
X-RAY DIFFRACTIONf_plane_restr0.003886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1451X-RAY DIFFRACTIONPOSITIONAL10.963
12D1451X-RAY DIFFRACTIONPOSITIONAL10.963
21B498X-RAY DIFFRACTIONPOSITIONAL10.963
22E498X-RAY DIFFRACTIONPOSITIONAL10.963
31C812X-RAY DIFFRACTIONPOSITIONAL10.963
32F812X-RAY DIFFRACTIONPOSITIONAL10.963
41G68X-RAY DIFFRACTIONPOSITIONAL10.963
42H68X-RAY DIFFRACTIONPOSITIONAL10.963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6121-2.71660.30361200.25652525X-RAY DIFFRACTION100
2.7166-2.84030.31551210.2472503X-RAY DIFFRACTION100
2.8403-2.990.30811320.24662494X-RAY DIFFRACTION100
2.99-3.17720.26841480.23492467X-RAY DIFFRACTION100
3.1772-3.42250.30331240.23462522X-RAY DIFFRACTION100
3.4225-3.76670.26661310.19992498X-RAY DIFFRACTION99
3.7667-4.31140.23031420.17832514X-RAY DIFFRACTION100
4.3114-5.43030.20941430.17692510X-RAY DIFFRACTION100
5.4303-43.84280.19351580.18432563X-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)
11.31740.3388-0.22460.93681.0931.5499-0.00970.13240.06470.1435-0.01020.2210.33530.1853-00.55690.09290.06080.56910.08790.4276-14.6295-24.0587-10.1915
20.38880.26240.17070.3205-0.03070.1248-0.1463-0.88840.4362-0.49440.8784-0.86120.30211.22020.00580.67130.1560.18541.22070.10820.9927-1.7095-18.4215-8.7096
31.72262.0009-1.18472.3588-1.11831.59170.4086-0.36780.28110.1963-0.22090.3221-0.27820.22780.01580.46390.03950.09130.53290.04050.4991-25.8214-23.3926-2.8812
40.73980.09610.12831.9885-0.62340.48530.52850.45970.40410.31850.02560.6601-0.1094-0.04620.00040.59580.0460.1310.75520.1410.7742-42.3959-30.04810.5934
50.5048-0.4211-0.52240.68430.55610.6552-0.50270.36790.5173-0.27540.54660.8541-0.6891-0.2964-0.44521.0301-0.0437-0.03230.50010.25270.8479-13.50569.1211-39.9624
60.1916-0.0921-0.17860.12510.06580.1763-0.15790.33420.1180.31780.38620.3154-0.1216-0.83670.00690.6680.08060.05380.5820.21620.4801-18.6266-3.2385-26.2041
71.3496-0.17240.64932.5987-0.61930.9233-0.4826-0.44350.3511-0.2098-0.0387-0.4746-0.0315-0.2024-0.06710.4240.20160.01090.89580.560.6424-24.0307-16.5137-15.0659
80.33680.04410.15980.1427-0.00240.49070.21420.2387-0.0604-0.0755-0.18730.14460.35890.3106-0.00010.56290.03680.00760.64230.20860.6269-31.9273-29.7928-3.97
90.2244-0.06010.06030.16670.15220.1890.2022-0.286-0.0259-0.02820.1388-0.5572-0.39930.1885-0.00120.5979-0.06580.02340.46690.00940.4509-3.8577-1.166-38.282
100.3933-0.32740.22780.83450.04970.24290.012-0.1125-0.12640.7287-0.0889-0.09440.55041.1568-0.58430.57910.2408-0.39580.96110.2094-0.3769-4.91851.4322-24.7988
110.20380.0444-0.04140.0412-0.03190.01480.7017-0.7911-0.090.21940.04040.0303-0.27550.47720.0060.89910.37230.13540.93780.09130.496-15.50673.0215-17.2657
121.3384-0.61030.68880.2662-0.27240.28660.5331-0.3121-0.66370.2435-0.56160.7668-0.3124-0.21890.01250.93870.34260.21521.28450.17320.8535-29.2967-5.5698-16.7536
130.03860.03110.07410.00650.00790.08790.3944-0.6444-0.4598-0.15681.5206-0.40031.44751.43410.00751.42970.1362-0.42841.4125-0.36081.7012-28.5501-21.0034-24.2717
140.0228-0.0129-0.01010.0079-0.01250.0201-0.78650.3691-0.334-0.3982-0.04260.8272-0.6505-0.04720.00280.722-0.1119-0.16831.5752-0.14451.0518-29.7315-8.2981-27.948
150.1226-0.03490.30660.91040.36840.91240.75841.28270.0617-0.27680.0728-0.0782-0.6507-1.35530.0830.63020.3164-0.01751.18720.10560.8769-27.1684.7125-24.7144
162.63220.32731.57390.12830.00631.37250.4644-0.60011.0405-0.13-0.0833-0.5469-1.1014-0.54960.21190.84240.11690.08270.3435-0.16260.6467-10.589510.5908-30.6452
172.0141-0.11381.57811.39911.06391.8154-0.11840.2345-0.3276-0.06580.14410.0642-0.14690.277-00.4705-0.0244-0.00940.36250.01870.3896-4.7661-10.355-52.0019
182.3572-2.3907-0.34312.53930.86852.0030.3428-0.11190.2823-0.0976-0.2162-0.9937-0.33151.15010.44690.3916-0.0584-0.17510.72590.01130.63327.0058-10.9361-49.6094
191.6659-1.49911.22841.6465-0.10111.2077-0.00680.0709-0.4915-0.3427-0.11730.3163-0.09510.0318-0.00220.4877-0.0637-0.13060.4884-0.00410.4445-22.0394-8.7208-58.193
200.32920.44450.06311.1431-0.73690.93470.29640.1493-0.2815-0.8701-0.11880.9414-0.4102-0.56120.020.81820.0699-0.22480.741-0.0321.0027-34.5457-3.1141-64.6336
210.0073-0.0108-0.01880.01270.01010.0328-0.4909-0.1749-0.1863-0.2846-0.716-0.36020.1974-0.14890.00621.92920.4346-0.19241.90610.70811.57011.1036-44.8663-19.2517
220.02140.0002-0.03290.0158-0.03880.0463-0.3459-0.3236-0.43330.9998-0.3550.40380.3575-0.7135-0.00041.2534-0.1368-0.13211.33720.21381.0847-3.678-37.6993-25.3916
231.6366-0.93520.22542.1722-0.13130.2373-0.5462-0.55750.7250.72750.38860.07650.2178-0.37510.02690.7585-0.03020.16910.60590.1810.8755-11.0321-24.462-40.6683
240.278-0.14570.16650.31630.26820.3147-0.509-0.45630.00030.26810.1456-0.0184-0.6495-0.0529-0.00060.450.0021-0.10480.4090.08320.6249-22.8883-3.8926-56.6015
250.0409-0.01770.01410.00020.00250.00310.2281-0.5122-0.0357-0.4147-0.3155-1.10780.2350.62920.00251.3191-0.0192-0.41381.826-0.18271.14845.8976-30.1418-27.9471
260.26640.1745-0.28850.4281-0.17240.50070.00520.8691-1.06230.05840.2523-0.45620.03231.115-0.00770.77150.0498-0.00840.84020.03090.67091.2828-33.9069-40.6507
270.10720.0632-0.05250.07750.0380.14310.14360.4281-0.12270.2849-0.48551.04190.0664-0.03960.00070.85360.02870.03330.52740.17120.798-15.7742-36.097-45.9434
280.1468-0.05110.19740.2686-0.06380.2082-0.252-0.59860.8559-0.02070.331.93590.6742-0.17650.00680.732-0.04490.07130.7344-0.04811.2032-22.0588-24.3866-44.0603
290.220.0991-0.17010.091-0.22610.532-0.7884-1.08570.29540.67470.5247-0.0645-0.27380.61-0.02240.98980.38230.21571.0617-0.35081.4521-19.589-14.1401-37.7286
300.2004-0.27870.3660.653-0.13580.89520.9834-0.15640.35240.17220.41120.5308-0.1067-0.48893.33281.4008-0.07381.22360.76750.46750.5903-19.7107-27.4331-34.2884
310.01780.0609-0.02450.96740.8721.25880.1617-0.5533-0.73810.1777-0.03510.30140.51170.25240.30480.93220.07660.09680.63510.3210.909-9.2877-42.2381-36.2865
321.62-0.9222-2.59960.51411.46924.14270.4431-0.20630.633-0.167-0.4227-0.7206-0.7814-0.17971.1590.8003-0.1058-0.55680.95630.31991.15396.0534-42.6455-29.1325
330.9709-1.70760.29733.1397-0.48680.1232-0.7231-0.1672-1.0115-0.57620.36150.63140.15490.1246-0.15230.61940.13360.13780.68130.18520.4399-11.4638-6.8736-26.357
340.5741-0.583-1.81040.9222.05795.8779-0.14390.26550.2979-1.5645-0.33920.01680.4147-0.87410.12271.1016-0.15960.26540.4211-0.01121.3214-2.91566.1522-41.3028
350.1835-0.0194-0.19480.00430.02490.21030.1804-0.23790.03380.1596-0.082-0.11340.3593-0.35350.00671.8727-0.346-0.44171.16910.29271.253410.6555-37.838-24.6669
360.56770.05720.08682.1670.63470.1858-0.27920.17290.56160.39690.595-1.010.4460.666-0.03310.7128-0.0719-0.12780.86560.20320.4631-1.4799-25.1226-36.0415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 13:59 )A13 - 59
2X-RAY DIFFRACTION2( CHAIN A AND RESID 60:73 )A60 - 73
3X-RAY DIFFRACTION3( CHAIN A AND RESID 74:120 )A74 - 120
4X-RAY DIFFRACTION4( CHAIN A AND RESID 121:161 )A121 - 161
5X-RAY DIFFRACTION5( CHAIN B AND RESID 756:763 )B756 - 763
6X-RAY DIFFRACTION6( CHAIN B AND RESID 764:780 )B764 - 780
7X-RAY DIFFRACTION7( CHAIN B AND RESID 781:788 )B781 - 788
8X-RAY DIFFRACTION8( CHAIN B AND RESID 789:805 )B789 - 805
9X-RAY DIFFRACTION9( CHAIN C AND RESID 2:12 )C2 - 12
10X-RAY DIFFRACTION10( CHAIN C AND RESID 13:22 )C13 - 22
11X-RAY DIFFRACTION11( CHAIN C AND RESID 23:31 )C23 - 31
12X-RAY DIFFRACTION12( CHAIN C AND RESID 32:50 )C32 - 50
13X-RAY DIFFRACTION13( CHAIN C AND RESID 51:62 )C51 - 62
14X-RAY DIFFRACTION14( CHAIN C AND RESID 63:68 )C63 - 68
15X-RAY DIFFRACTION15( CHAIN C AND RESID 69:81 )C69 - 81
16X-RAY DIFFRACTION16( CHAIN C AND RESID 82:95 )C82 - 95
17X-RAY DIFFRACTION17( CHAIN D AND RESID 13:65 )D13 - 65
18X-RAY DIFFRACTION18( CHAIN D AND RESID 66:79 )D66 - 79
19X-RAY DIFFRACTION19( CHAIN D AND RESID 80:129 )D80 - 129
20X-RAY DIFFRACTION20( CHAIN D AND RESID 130:161 )D130 - 161
21X-RAY DIFFRACTION21( CHAIN E AND RESID 755:758 )E755 - 758
22X-RAY DIFFRACTION22( CHAIN E AND RESID 759:767 )E759 - 767
23X-RAY DIFFRACTION23( CHAIN E AND RESID 768:787 )E768 - 787
24X-RAY DIFFRACTION24( CHAIN E AND RESID 788:805 )E788 - 805
25X-RAY DIFFRACTION25( CHAIN F AND RESID 8:12 )F8 - 12
26X-RAY DIFFRACTION26( CHAIN F AND RESID 13:30 )F13 - 30
27X-RAY DIFFRACTION27( CHAIN F AND RESID 31:39 )F31 - 39
28X-RAY DIFFRACTION28( CHAIN F AND RESID 40:49 )F40 - 49
29X-RAY DIFFRACTION29( CHAIN F AND RESID 50:60 )F50 - 60
30X-RAY DIFFRACTION30( CHAIN F AND RESID 61:72 )F61 - 72
31X-RAY DIFFRACTION31( CHAIN F AND RESID 73:87 )F73 - 87
32X-RAY DIFFRACTION32( CHAIN F AND RESID 88:95 )F88 - 95
33X-RAY DIFFRACTION33( CHAIN G AND RESID 331:339 )G331 - 339
34X-RAY DIFFRACTION34( CHAIN X AND RESID 325:330 )X325 - 330
35X-RAY DIFFRACTION35( CHAIN Y AND RESID 327:330 )Y327 - 330
36X-RAY DIFFRACTION36( CHAIN H AND RESID 330:339 )H330 - 339

+
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