[English] 日本語
Yorodumi
- PDB-4kvm: The NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kvm
TitleThe NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex bound to a bisubstrate analog
Components
  • (N-terminal acetyltransferase A complex ...) x 2
  • bisubstrate analog inhibitor
Keywordstransferase/transferase inhibitor / Acetyltransferase / TPR repeats / amino-terminal acetylation / transferase-transferase inhibitor complex
Function / homology
Function and homology information


protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / acetyltransferase activator activity / protein maturation / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1010 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1010 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Aminopeptidase / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1XE / N-terminal acetyltransferase A complex subunit nat1 / N-terminal acetyltransferase A complex catalytic subunit ard1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsLiszczak, G.P. / Marmorstein, R.Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.
Authors: Liszczak, G. / Goldberg, J.M. / Foyn, H. / Petersson, E.J. / Arnesen, T. / Marmorstein, R.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 2.0Sep 22, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_ec / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-terminal acetyltransferase A complex subunit nat1
B: N-terminal acetyltransferase A complex subunit nat1
C: N-terminal acetyltransferase A complex subunit nat1
D: N-terminal acetyltransferase A complex subunit nat1
E: N-terminal acetyltransferase A complex catalytic subunit ard1
F: N-terminal acetyltransferase A complex catalytic subunit ard1
G: N-terminal acetyltransferase A complex catalytic subunit ard1
H: N-terminal acetyltransferase A complex catalytic subunit ard1
I: bisubstrate analog inhibitor
J: bisubstrate analog inhibitor
K: bisubstrate analog inhibitor
L: bisubstrate analog inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,05982
Polymers410,31212
Non-polymers5,74770
Water5,855325
1
A: N-terminal acetyltransferase A complex subunit nat1
E: N-terminal acetyltransferase A complex catalytic subunit ard1
I: bisubstrate analog inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,09822
Polymers102,5783
Non-polymers1,52019
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-terminal acetyltransferase A complex subunit nat1
F: N-terminal acetyltransferase A complex catalytic subunit ard1
J: bisubstrate analog inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,00221
Polymers102,5783
Non-polymers1,42418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-terminal acetyltransferase A complex subunit nat1
G: N-terminal acetyltransferase A complex catalytic subunit ard1
K: bisubstrate analog inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,89618
Polymers102,5783
Non-polymers1,31815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-terminal acetyltransferase A complex subunit nat1
H: N-terminal acetyltransferase A complex catalytic subunit ard1
L: bisubstrate analog inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,06321
Polymers102,5783
Non-polymers1,48518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.439, 119.381, 134.063
Angle α, β, γ (deg.)80.20, 76.60, 70.42
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 100:632 or resseq 642:731 )
211chain 'B' and (resseq 100:632 or resseq 642:731 )
311chain 'C' and (resseq 100:632 or resseq 642:731 )
411chain 'D' and (resseq 100:632 or resseq 642:731 )
112chain 'E' and (resseq 1:153 )
212chain 'F' and (resseq 1:153 )
312chain 'G' and (resseq 1:153 )
412chain 'H' and (resseq 1:153 )

NCS ensembles :
ID
1
2

-
Components

-
N-terminal acetyltransferase A complex ... , 2 types, 8 molecules ABCDEFGH

#1: Protein
N-terminal acetyltransferase A complex subunit nat1 / NatA complex subunit nat1


Mass: 84154.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: nat1, SPCC338.07c / Production host: Escherichia coli (E. coli) / References: UniProt: O74985
#2: Protein
N-terminal acetyltransferase A complex catalytic subunit ard1 / NatA complex subunit ARD1


Mass: 18030.750 Da / Num. of mol.: 4 / Fragment: unp residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: ard1, SPAC15E1.08 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UTI3, N-terminal amino-acid Nalpha-acetyltransferase NatA

-
Protein/peptide , 1 types, 4 molecules IJKL

#3: Protein/peptide
bisubstrate analog inhibitor


Mass: 392.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 395 molecules

#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-1XE / [5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate


Mass: 821.538 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H34N7O18P3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Buffer: 25 mM Hepes, pH 7.0, 200 mM NaCl, 1 mM TCEP Crystallization buffer: 100 mM Hepes, pH 7.0, 10% Peg 4000, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2012 / Details: Si-111 double crystal monochromator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 137695 / Num. obs: 137534

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4KVX

4kvx


Resolution: 2.597→49.59 Å / SU ML: 0.44 / σ(F): 1.96 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 6906 5.02 %
Rwork0.2216 --
obs0.2235 137534 96.85 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.832 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-29.535 Å2-2.238 Å24.8581 Å2
2---25.4792 Å2-1.1654 Å2
3----4.0558 Å2
Refinement stepCycle: LAST / Resolution: 2.597→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28076 0 278 325 28679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828960
X-RAY DIFFRACTIONf_angle_d1.16639102
X-RAY DIFFRACTIONf_dihedral_angle_d16.94910928
X-RAY DIFFRACTIONf_chiral_restr0.0864227
X-RAY DIFFRACTIONf_plane_restr0.0054991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4984X-RAY DIFFRACTIONPOSITIONAL
12B4984X-RAY DIFFRACTIONPOSITIONAL0.044
13C4941X-RAY DIFFRACTIONPOSITIONAL0.053
14D4963X-RAY DIFFRACTIONPOSITIONAL0.036
21E1231X-RAY DIFFRACTIONPOSITIONAL
22F1231X-RAY DIFFRACTIONPOSITIONAL0.043
23G1231X-RAY DIFFRACTIONPOSITIONAL0.045
24H1231X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5974-2.62690.36191900.34223311X-RAY DIFFRACTION74
2.6269-2.65780.41191900.3323914X-RAY DIFFRACTION87
2.6578-2.69020.34652100.34654029X-RAY DIFFRACTION90
2.6902-2.72430.36592330.32284195X-RAY DIFFRACTION93
2.7243-2.76010.34342290.30924219X-RAY DIFFRACTION96
2.7601-2.79790.3152230.30794455X-RAY DIFFRACTION97
2.7979-2.83790.35432340.30764400X-RAY DIFFRACTION98
2.8379-2.88030.34432110.30584378X-RAY DIFFRACTION98
2.8803-2.92530.35162650.29544449X-RAY DIFFRACTION98
2.9253-2.97320.28552350.27894397X-RAY DIFFRACTION98
2.9732-3.02450.33822350.27934402X-RAY DIFFRACTION98
3.0245-3.07950.30822060.28344444X-RAY DIFFRACTION98
3.0795-3.13870.33852420.27724420X-RAY DIFFRACTION98
3.1387-3.20270.31822480.27564375X-RAY DIFFRACTION98
3.2027-3.27240.30632170.27094464X-RAY DIFFRACTION98
3.2724-3.34850.30842300.26584415X-RAY DIFFRACTION98
3.3485-3.43220.31592640.26984442X-RAY DIFFRACTION99
3.4322-3.5250.32822330.26044446X-RAY DIFFRACTION99
3.525-3.62870.29772190.25294443X-RAY DIFFRACTION99
3.6287-3.74570.29382430.24144432X-RAY DIFFRACTION99
3.7457-3.87960.27022340.24354476X-RAY DIFFRACTION99
3.8796-4.03480.26672290.22734409X-RAY DIFFRACTION99
4.0348-4.21840.2332430.2014439X-RAY DIFFRACTION99
4.2184-4.44060.19762320.18194458X-RAY DIFFRACTION99
4.4406-4.71870.22682250.17684474X-RAY DIFFRACTION99
4.7187-5.08270.21032340.17844472X-RAY DIFFRACTION99
5.0827-5.59350.21292480.19194462X-RAY DIFFRACTION99
5.5935-6.40150.28242310.22764497X-RAY DIFFRACTION100
6.4015-8.05960.22072410.17984472X-RAY DIFFRACTION100
8.0596-49.59920.20842320.1724439X-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)
14.1028-0.4968-1.06821.1851-0.32890.88550.3476-0.09150.34120.1192-0.1917-0.3651-0.2050.3277-0.13940.5812-0.18650.00010.5505-0.09790.5248-22.47329.3058-75.222
22.1085-1.5747-0.80827.1473-1.55491.63730.2495-0.2976-0.3985-0.09750.12461.07670.0121-0.1526-0.37820.6419-0.1011-0.01740.68080.08030.6861-67.4317-4.0499-54.9502
31.44030.676-0.20463.1777-1.45321.4147-0.1048-0.0084-0.2262-0.24920.20810.03140.17860.0046-0.10030.5917-0.127-0.01210.5624-0.04060.449-37.0185-14.694-63.7184
42.8327-0.6532-0.164.68690.60862.2923-0.3493-0.3997-0.37481.19410.3444-0.5057-0.18360.28340.03410.96990.0111-0.13680.63190.00550.5515-23.4672-20.5999-46.3397
53.1643-0.59890.1822.78560.45921.7029-0.73220.201-0.0291-0.00720.3406-0.6852-0.8032-0.00410.11410.3477-0.34220.1020.41080.0690.6335-11.327768.8885-79.0369
62.78061.20680.31740.62530.19310.87240.20480.538-0.6176-0.48880.6484-1.3179-0.04950.93580.62440.6633-0.08290.80051.4866-0.55351.945516.021329.6563-99.2112
70.90720.45490.66743.72910.37220.70980.0110.1789-0.2285-0.1615-0.0321-0.34620.02650.10030.04960.4539-0.15180.19050.619-0.02940.5322-14.51140.5659-90.5344
84.23530.7412-0.47174.4308-0.283.5075-0.28480.89420.1554-1.4690.11610.5967-0.6365-0.41280.15911.002-0.1315-0.06570.7963-0.05320.5568-28.719344.5593-107.9859
93.83180.1055-0.04062.86310.59821.7043-0.43350.04130.00240.11770.3364-0.6630.4574-0.0333-0.0060.5330.2969-0.17270.5264-0.0350.7467-41.8666-48.5124-140.9496
102.405-0.5976-0.50050.17310.06110.88310.4735-0.27380.80430.69060.2736-1.67330.01820.7066-0.5050.8557-0.0965-0.43071.2267-0.48122.0553-15.6934-8.5084-121.3334
111.6201-0.8832-1.17933.76621.5931.54760.3660.20630.3726-0.1546-0.1931-0.5602-0.04090.1099-0.1570.47610.2103-0.10270.58040.04060.5667-45.7456-20.4603-130.1901
123.7671-1.32190.53014.4866-0.17222.6275-0.2337-0.35290.10331.1460.05840.51450.9181-0.13830.09720.95490.16240.10570.5710.00260.6206-60.0245-24.3624-112.7679
133.93470.31610.71512.1158-0.88521.00840.31860.0616-0.2422-0.8129-0.3546-0.64610.40630.37610.02280.95480.35180.34250.62510.07410.6913-23.090424.3349-14.9421
141.97310.34641.30216.6339-1.11061.32640.32030.1017-0.02180.32620.04220.53060.3299-0.2225-0.34640.95930.0594-0.03420.75980.0530.5538-68.502937.5562-35.2609
151.6761-0.7974-0.04992.3017-1.55991.589-0.1931-0.0025-0.0161-0.1436-0.00750.05820.12060.14910.20920.82860.17740.01070.5704-0.0580.5043-37.86648.0189-26.3412
163.17851.01850.02494.2180.17892.3579-0.55350.54420.075-1.26610.359-0.34490.60590.29330.14081.18790.07870.17370.68080.04070.5963-24.506854.2464-43.9804
174.4868-0.1783-0.38446.3592-0.97931.44750.3314-0.03030.09690.1186-0.1910.30980.16830.0047-0.16910.4287-0.1422-0.01040.4889-0.10310.3358-45.7445-1.4947-74.8082
181.77641.75730.36192.26420.44411.25780.14230.3252-0.1598-0.8999-0.05781.22240.5113-0.3849-0.12740.8492-0.1299-0.11930.7285-0.12580.7913-52.2893-6.3442-87.3115
194.8163-0.25510.75033.6458-0.41380.743-0.1077-0.1381-1.0189-0.16910.0449-1.63990.12660.2626-0.01860.4667-0.12940.08540.71740.06611.29880.601745.4662-79.0614
202.53193.13930.0255.41140.09342.07240.2247-0.4868-1.27781.292-0.2676-1.56940.60130.3644-0.03080.892-0.0815-0.36520.95710.4181.76392.307437.1027-66.6203
215.2113-0.5457-1.00734.3169-0.44711.3430.13550.18311.39130.06350.0767-1.6854-0.34170.1145-0.16820.5220.189-0.00720.6752-0.01321.3415-30.5757-25.0876-141.6012
222.5235-2.6121.45166.3016-0.12623.17460.03280.84941.3043-1.038-0.1493-0.7861-0.90250.135-0.0530.96720.23630.45820.95980.45031.7871-29.041-16.9295-154.2056
234.99630.3922-0.86286.5336-0.87952.06470.1628-0.05110.0193-0.7257-0.15260.54280.0244-0.0317-0.02470.57060.1959-0.04680.5145-0.07890.3979-46.435134.8761-15.2502
242.3256-1.9498-0.57872.1882-0.09131.74250.2146-0.34840.29620.27460.00041.3439-0.5058-0.3664-0.26720.70580.17250.02480.7764-0.1050.9578-53.091439.8761-2.8024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:269)
2X-RAY DIFFRACTION2(chain A and resid 270:428)
3X-RAY DIFFRACTION3(chain A and resid 429:572)
4X-RAY DIFFRACTION4(chain A and resid 573:731)
5X-RAY DIFFRACTION5(chain B and resid 5:266)
6X-RAY DIFFRACTION6(chain B and resid 267:428)
7X-RAY DIFFRACTION7(chain B and resid 429:572)
8X-RAY DIFFRACTION8(chain B and resid 573:731)
9X-RAY DIFFRACTION9(chain C and resid 5:269)
10X-RAY DIFFRACTION10(chain C and resid 270:428)
11X-RAY DIFFRACTION11(chain C and resid 429:572)
12X-RAY DIFFRACTION12(chain C and resid 573:731)
13X-RAY DIFFRACTION13(chain D and resid 5:269)
14X-RAY DIFFRACTION14(chain D and resid 270:428)
15X-RAY DIFFRACTION15(chain D and resid 429:572)
16X-RAY DIFFRACTION16(chain D and resid 573:731)
17X-RAY DIFFRACTION17(chain E and resid 1:97)
18X-RAY DIFFRACTION18(chain E and resid 98:153)
19X-RAY DIFFRACTION19(chain F and resid 1:99)
20X-RAY DIFFRACTION20(chain F and resid 100:153)
21X-RAY DIFFRACTION21(chain G and resid 1:99)
22X-RAY DIFFRACTION22(chain G and resid 100:153)
23X-RAY DIFFRACTION23(chain H and resid 1:98)
24X-RAY DIFFRACTION24(chain H and resid 99:153)

+
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