[English] 日本語
Yorodumi
- PDB-6u9d: Saccharomyces cerevisiae acetohydroxyacid synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u9d
TitleSaccharomyces cerevisiae acetohydroxyacid synthase
Components(Acetolactate synthase ...) x 2
KeywordsTRANSFERASE / AHAS / pyruvate / FAD / dioxygen
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / mitochondrial nucleoid / amino acid biosynthetic process ...acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / mitochondrial nucleoid / amino acid biosynthetic process / enzyme regulator activity / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion
Similarity search - Function
Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site ...Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / Acetolactate synthase/Transcription factor NikR, C-terminal / Acetolactate synthase, large subunit, biosynthetic / Acetolactate synthase large subunit, TPP binding domain / ACT domain / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / ACT domain profile. / ACT domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / ACT-like domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-60G / ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetohydroxy-acid synthase small subunit / Acetolactate synthase catalytic subunit, mitochondrial / Acetolactate synthase small subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.194 Å
AuthorsGuddat, L.W. / Lonhienne, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Grant numbers 1087713 & 1147297 Australia
CitationJournal: Nature / Year: 2020
Title: Structures of fungal and plant acetohydroxyacid synthases.
Authors: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J ...Authors: Thierry Lonhienne / Yu Shang Low / Mario D Garcia / Tristan Croll / Yan Gao / Quan Wang / Lou Brillault / Craig M Williams / James A Fraser / Ross P McGeary / Nicholas P West / Michael J Landsberg / Zihe Rao / Gerhard Schenk / Luke W Guddat /
Abstract: Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the ...Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the biosynthesis of branched-chain amino acids. It is the target for more than 50 commercial herbicides. AHAS requires both catalytic and regulatory subunits for maximal activity and functionality. Here we describe structures of the hexadecameric AHAS complexes of Saccharomyces cerevisiae and dodecameric AHAS complexes of Arabidopsis thaliana. We found that the regulatory subunits of these AHAS complexes form a core to which the catalytic subunit dimers are attached, adopting the shape of a Maltese cross. The structures show how the catalytic and regulatory subunits communicate with each other to provide a pathway for activation and for feedback inhibition by branched-chain amino acids. We also show that the AHAS complex of Mycobacterium tuberculosis adopts a similar structure, thus demonstrating that the overall AHAS architecture is conserved across kingdoms.
History
DepositionSep 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: 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
Revision 1.2Oct 21, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Revision 1.3Jan 27, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 11, 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: Acetolactate synthase catalytic subunit, mitochondrial
B: Acetolactate synthase catalytic subunit, mitochondrial
C: Acetolactate synthase small subunit, mitochondrial
D: Acetolactate synthase small subunit, mitochondrial
E: Acetolactate synthase catalytic subunit, mitochondrial
F: Acetolactate synthase catalytic subunit, mitochondrial
G: Acetolactate synthase small subunit, mitochondrial
H: Acetolactate synthase small subunit, mitochondrial
I: Acetolactate synthase catalytic subunit, mitochondrial
J: Acetolactate synthase catalytic subunit, mitochondrial
K: Acetolactate synthase small subunit, mitochondrial
L: Acetolactate synthase small subunit, mitochondrial
M: Acetolactate synthase catalytic subunit, mitochondrial
N: Acetolactate synthase catalytic subunit, mitochondrial
O: Acetolactate synthase small subunit, mitochondrial
P: Acetolactate synthase small subunit, mitochondrial
Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,261,92587
Polymers1,236,42024
Non-polymers25,50563
Water79344
1
A: Acetolactate synthase catalytic subunit, mitochondrial
B: Acetolactate synthase catalytic subunit, mitochondrial
C: Acetolactate synthase small subunit, mitochondrial
D: Acetolactate synthase small subunit, mitochondrial
E: Acetolactate synthase catalytic subunit, mitochondrial
F: Acetolactate synthase catalytic subunit, mitochondrial
G: Acetolactate synthase small subunit, mitochondrial
H: Acetolactate synthase small subunit, mitochondrial
I: Acetolactate synthase catalytic subunit, mitochondrial
J: Acetolactate synthase catalytic subunit, mitochondrial
K: Acetolactate synthase small subunit, mitochondrial
L: Acetolactate synthase small subunit, mitochondrial
M: Acetolactate synthase catalytic subunit, mitochondrial
N: Acetolactate synthase catalytic subunit, mitochondrial
O: Acetolactate synthase small subunit, mitochondrial
P: Acetolactate synthase small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)841,59960
Polymers824,28016
Non-polymers17,31944
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area117230 Å2
ΔGint-751 kcal/mol
Surface area228780 Å2
MethodPISA
2
Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
hetero molecules

Q: Acetolactate synthase catalytic subunit, mitochondrial
R: Acetolactate synthase catalytic subunit, mitochondrial
S: Acetolactate synthase small subunit, mitochondrial
T: Acetolactate synthase small subunit, mitochondrial
U: Acetolactate synthase catalytic subunit, mitochondrial
V: Acetolactate synthase catalytic subunit, mitochondrial
W: Acetolactate synthase small subunit, mitochondrial
X: Acetolactate synthase small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)840,65154
Polymers824,28016
Non-polymers16,37138
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area109200 Å2
ΔGint-693 kcal/mol
Surface area224660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)368.647, 230.307, 183.532
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Acetolactate synthase ... , 2 types, 24 molecules ABEFIJMNQRUVCDGHKLOPSTWX

#1: Protein
Acetolactate synthase catalytic subunit, mitochondrial / Acetohydroxy-acid synthase catalytic subunit / ALS


Mass: 70264.992 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ILV2, SMR1, YMR108W, YM9718.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P07342, acetolactate synthase
#2: Protein
Acetolactate synthase small subunit, mitochondrial


Mass: 32770.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ilv2 / Production host: Escherichia coli (E. coli) / References: UniProt: B3LU66, UniProt: P25605*PLUS

-
Non-polymers , 6 types, 107 molecules

#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Chemical
ChemComp-60G / methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate / Bensulfuron methyl


Mass: 410.402 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H18N4O7S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: The crystals of Saccharomyces cerevisiae AHAS complex were obtained by the hanging drop vapor diffusion method. The catalytic subunit (70.527 kDa, 70 mg/ml) and regulatory subunit (29.625 ...Details: The crystals of Saccharomyces cerevisiae AHAS complex were obtained by the hanging drop vapor diffusion method. The catalytic subunit (70.527 kDa, 70 mg/ml) and regulatory subunit (29.625 kDa, 19.8 mg/ml) freshly thawed were mixed together in a ratio of 1:2, giving a solution where the concentration of the RSU was ~ 30% in excess compared to the CSU. The cofactors, inhibitor, and DTT were added to the solution to a final concentration of 2 mM ThDP, 1 mM FAD, 10 mM MgCl2, 1 mM BSM and 5 mM DTT. The crystallization buffer consisted of 0.2 M sodium malonate pH 7 and 20% w/v PEG 3,350. The crystallization drops consisted of equal volumes (1 ul) of well solution and enzyme complex

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 26, 2018 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.19→49.115 Å / Num. obs: 250942 / % possible obs: 99.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 68.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.054 / Rrim(I) all: 0.151 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.19-3.257.50.77390467120140.8330.2990.829296.5
17.49-49.116.70.0341010015110.9970.0150.03738.394.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BSM complex18 (PDB code 5FEM) and the RSU of Thermotoga maritima16 (PDB code 2FGC).

5fem

2fgc


Resolution: 3.194→49.11 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1997 0.8 %1997
Rwork0.2049 ---
obs0.2053 250831 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 234.67 Å2 / Biso mean: 74.3925 Å2 / Biso min: 1.78 Å2
Refinement stepCycle: final / Resolution: 3.194→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76015 0 1593 44 77652
Biso mean--59.44 48.52 -
Num. residues----10005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00279237
X-RAY DIFFRACTIONf_angle_d0.585107934
X-RAY DIFFRACTIONf_chiral_restr0.02112353
X-RAY DIFFRACTIONf_plane_restr0.00313889
X-RAY DIFFRACTIONf_dihedral_angle_d13.26429101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.194-3.27360.31311410.27921732797
3.2736-3.36210.32321430.27471767599
3.3621-3.4610.32491380.26281775199
3.461-3.57270.31891460.248717725100
3.5727-3.70030.24671390.23531771499
3.7003-3.84840.28551440.231117732100
3.8484-4.02350.2411390.214617835100
4.0235-4.23550.25791410.194917731100
4.2355-4.50070.24271520.180317822100
4.5007-4.84790.221380.170917834100
4.8479-5.33530.22451430.175917845100
5.3353-6.10610.25481460.207817914100
6.1061-7.68820.25421460.199917916100
7.6882-49.110.2061410.17341801399
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)
11.7113-0.0077-0.98271.20210.28952.30970.06460.14610.3121-0.0447-0.14160.035-0.3176-0.154-0.20190.2306-0.0081-0.06220.40070.04660.3701306.46645.5026175.8783
21.5023-0.26970.05491.5367-0.19351.3225-0.1164-0.4504-0.02970.5456-0.02060.1771-0.07-0.3415-0.04420.45-0.06360.03320.5483-0.02460.3203295.990936.3456202.3215
32.34840.0673-0.67592.70220.01631.5695-0.0160.1645-0.3934-0.1351-0.13010.49050.161-0.5308-0.13680.2339-0.03560.00830.4595-0.00890.4811289.318815.9358176.4454
41.45030.04890.31131.55650.01831.73720.11790.43-0.2782-0.2722-0.1115-0.33060.3120.316-0.21420.32570.06380.05590.4449-0.01250.5222319.699211.0673164.1393
51.3594-0.1027-2.08373.1993-0.31653.27240.35810.37260.24440.33120.0345-0.39880.48910.54670.1580.52190.08620.14690.8339-0.04251.0277238.549939.333153.9268
60.18910.27160.81925.0279-0.62584.26490.0624-0.0774-0.06570.0116-0.04460.49880.1955-0.188-0.01940.28550.0415-0.07320.5928-0.01780.4884283.512846.5305166.3434
72.02741.79250.69758.23053.74763.34970.02910.1655-0.35520.3366-0.06850.03170.26360.0195-0.10270.28610.0266-0.02870.6217-0.00920.4383264.646332.3607146.1499
82.75351.4463-1.45582.5790.38191.48610.09920.02020.44580.3901-0.1893-0.1726-0.23130.29480.26560.85490.19740.22941.3202-0.1580.7022291.29861.0095117.9782
93.62860.0546-3.64845.2981-0.37944.15160.10890.1061-0.0446-0.1124-0.1293-0.09440.0268-0.2573-0.05470.36220.0489-0.14870.6221-0.00880.4837288.947429.1954152.0465
101.384-1.0545-0.64164.899-1.1371.0280.040.2105-0.03570.2509-0.0462-0.26-0.11130.1805-0.02550.31990.0337-0.16580.65940.00290.4539281.803759.1749144.6007
112.1748-0.051.42131.5241-0.26862.625-0.3183-0.32210.490.0946-0.0063-0.0119-0.3072-0.20780.32520.54790.10950.02170.8786-0.02460.5406305.379547.909287.408
121.18830.20160.44641.2462-0.01260.9168-0.0882-0.0847-0.2080.0960.0624-0.44610.32320.29410.04660.61710.1739-0.00650.90010.00130.6548325.416424.615994.539
131.4783-0.36361.3733.7971-0.11052.1401-0.0157-0.3059-0.26550.26580.02730.27060.3327-0.57920.02180.6804-0.00450.11270.9137-0.04920.4694292.967116.427990.2218
141.1157-0.1131-0.06271.04030.07171.4112-0.11060.4989-0.0196-0.3613-0.07360.13890.137-0.62540.00370.7411-0.04710.03041.1956-0.0840.4827285.761730.93461.4883
150.82150.5031.32925.34590.34192.4066-0.00680.6713-0.2632-0.32840.229-0.2967-0.1114-0.10280.14620.6230.0522-0.11990.7830.10820.5987272.429622.9367144.244
162.59650.6943-0.92040.978-0.27491.0798-0.18390.4754-0.3431-0.13850.0522-0.17280.19170.0582-0.03910.53570.02080.01660.9346-0.19870.5086276.744835.7537116.8105
170.62920.8522-0.31953.4105-1.78570.97750.2168-0.02780.05920.5205-0.09891.0114-1.0578-0.46980.2130.79670.16890.16161.04550.0390.795256.600187.6657126.4853
180.27740.8169-0.14972.8007-0.45790.08690.94410.6262-0.6509-1.7983-0.565-0.1576-0.06150.19270.30961.21740.0432-0.40831.6449-0.00170.9258262.582170.0471100.5374
190.58110.0073-0.20342.53871.23221.7642-0.10490.4315-0.0438-0.44030.1213-0.1218-0.00730.038-0.13590.4696-0.03340.03471.058-0.02730.4385278.284452.2142110.9585
201.2054-0.4922-1.35634.2958-0.05061.69360.1526-0.24120.3415-0.1171-0.22080.0339-0.35950.3468-0.11210.54880.0335-0.20040.9521-0.05160.6068227.104789.237392.1129
213.1568-0.09890.06032.2563-0.33440.07630.01950.39560.2687-0.5081-0.1161-0.4896-0.28990.4173-0.02231.02240.0044-0.01031.33640.10990.6487252.67380.691672.9516
220.94650.1981-0.2311.48240.09050.9691-0.15070.4920.0901-0.9046-0.10050.1370.01590.23160.01081.27820.0717-0.15951.27960.00360.54231.599373.688462.4629
231.1171-0.2653-0.29691.9034-0.14621.4186-0.0228-0.1783-0.0476-0.0638-0.07340.7470.1484-0.4169-0.05810.4469-0.0129-0.10871.2629-0.20680.7652207.82763.7936100.1638
240.36050.4148-0.13311.1766-0.22040.7720.13850.27630.2022-0.3634-0.06171.1612-0.2296-0.67520.10360.7030.1929-0.3961.4264-0.17381.2995196.941285.329587.5698
251.7360.0611-0.0524.1915-1.47312.00760.2657-0.41370.0260.52970.179-0.08840.24480.36280.03210.77660.03190.03131.1894-0.08310.6002265.886420.6661115.8811
262.4926-1.43340.69442.1999-1.89581.7673-0.13970.1633-0.2079-0.9690.14670.82290.1577-0.4429-0.00650.5645-0.1052-0.16891.18810.15460.704245.422162.656598.7746
270.2357-0.168-0.05852.5855-1.41291.6238-0.01140.4422-0.1685-0.2743-0.05390.07570.1236-0.0896-0.12370.4278-0.0146-0.13951.0287-0.08220.5439242.98450.4415113.7511
280.01020.01010.0040.00980.01650.0128-0.3289-0.103-0.2067-0.3354-0.114-0.52320.12980.71440.03440.91020.12510.05971.4610.16280.8686271.284664.04104.2042
293.24260.11110.23512.29010.49791.00570.429-1.4827-0.16341.04310.0252-0.6764-0.05260.4967-0.17060.69950.0512-0.06321.2804-0.05270.7176271.009279.381155.418
303.80121.20413.39671.11811.27043.0014-0.47490.14670.9687-0.6253-0.38140.5682-0.9729-0.86520.96750.5546-0.02810.06551.1880.02640.7314236.399673.141129.4101
312.0466-0.4793-0.09774.51360.26611.26420.154-0.08640.13420.1038-0.14950.23530.0643-0.0838-0.12020.44560.0117-0.05971.2535-0.00590.634227.793763.7621112.6284
323.3731.699-0.11092.42540.6071.3444-0.0470.48320.3371-0.3124-0.07220.1555-0.2799-0.0945-0.15850.4590.0685-0.1530.94870.15580.5256260.070275.3247119.1893
335.0964-0.07422.4165.7055-1.08931.3514-0.1748-0.36060.0445-0.08780.27890.66570.1966-0.3748-0.36750.9807-0.07480.07291.3861-0.01340.7983227.292852.1849141.5225
342.1431-0.50310.15722.6863-0.26492.20940.06020.16450.3522-0.0739-0.1429-0.423-0.09620.5263-0.01670.2856-0.0666-0.04270.4171-0.01060.4621233.766686.3707176.3874
351.8528-0.4072-0.42971.73260.12641.37440.07660.49260.1368-0.0944-0.31680.6181-0.1884-0.4-0.29840.3106-0.0072-0.08610.5112-0.13290.7421203.154190.2151168.9824
361.34010.11950.84431.3473-0.14041.1849-0.12920.175-0.60190.1081-0.13170.31030.5519-0.1101-0.1060.4241-0.09130.19340.431-0.17010.766212.998360.5224175.0774
374.4768-2.48913.4922.2878-1.33453.13610.24160.2895-1.03890.2712-0.14040.43950.968-0.0148-0.85361.05980.00290.09380.8248-0.01851.0702229.713440.6692175.0818
381.5094-0.45570.03622.03760.09361.1246-0.1527-0.6501-0.38840.9016-0.00030.05310.48450.3606-0.09180.95870.02270.06510.72090.18040.5614227.714960.5467202.903
396.0331-2.79711.7444.8586-1.84833.0041-0.6941-1.07380.50671.5813-0.0167-0.6204-0.05020.2284-0.09061.15680.024-0.24911.20510.03550.6935239.135978.2382211.2374
405.2610.5871-1.53298.89221.83926.802-0.20730.2306-0.25430.0344-0.04990.8193-0.1185-0.48040.20680.5222-0.0126-0.24921.2188-0.0381.0591229.108944.3863115.3689
412.0362-0.5367-1.55846.85923.35293.5296-0.2595-0.2997-0.2986-1.1571-0.65640.94330.3072-1.6508-0.10640.7332-0.053-0.03520.946-0.14680.6414233.100568.7707147.0924
427.40.06710.3055.2895-0.22651.190.1160.3225-0.1965-0.1578-0.08250.2410.1405-0.0609-0.0550.40820.01860.0450.5416-0.03440.355234.39673.6583153.9135
430.5998-0.79420.41366.03080.36640.8130.03340.163-0.15390.4675-0.03380.50690.2416-0.17930.02130.3538-0.04440.08410.7105-0.10610.5701242.649941.3968146.0847
445.44810.38163.62594.7854-2.12743.6049-0.028-0.32540.6412-0.0441-0.3912-0.6920.41831.3703-0.22461.36160.43140.27392.01280.24930.8441243.918779.9709125.5909
450.70370.5771-2.27480.4916-1.90267.40660.3170.5210.1307-0.2171-0.1081-0.0758-0.27920.4111-0.06270.6502-0.0827-0.14561.19710.04440.5905294.938666.4311138.8335
464.11711.3536-0.14090.4544-0.06120.00530.0595-0.17830.38560.213-0.0990.11950.01950.0689-0.13980.4014-0.0189-0.10720.6421-0.02510.7154268.105358.6057164.1578
470.748-0.2914-0.72271.6020.10271.61740.02390.0247-0.12950.1952-0.01610.1049-0.1832-0.0965-0.02870.3860.0280.06010.5639-0.05710.4957239.760657.3828167.3459
481.14590.1695-0.36440.5223-0.00940.94120.1170.06610.17060.0907-0.06350.1712-0.0925-0.0159-0.08530.33080.0581-0.01380.51720.00050.4573257.641868.3404149.2337
491.2899-0.53280.07012.09340.44241.02040.25870.26890.119-0.9691-0.02250.14370.0185-0.2628-0.10680.9214-0.0401-0.09670.37930.14780.502337.4138158.6569145.5412
500.9681-0.1614-0.00931.2092-0.16470.61650.222-0.25631.3314-1.11090.2124-0.6362-0.61760.16280.23521.26-0.14080.5342-0.08730.40641.0105350.8225179.614146.7342
510.699-0.3048-0.24120.21290.02760.86340.1390.35060.3554-1.1080.0561-0.9490.23310.51690.52391.3158-0.18110.93510.4590.07840.874369.3865156.2694140.7943
520.2912-0.3703-0.22610.8080.66630.50090.16310.4223-0.0265-0.9418-0.1301-0.38990.12990.038-0.39631.9519-0.0020.37610.7838-0.25310.8049368.7196130.2442123.9393
530.40290.08250.18930.01440.03620.083-0.13220.5427-0.3992-0.59880.0603-0.30.20830.09260.28551.9050.07150.51160.9899-0.13350.8135368.0598135.4253118.5423
540.77170.05770.19840.3797-0.17210.74390.53270.61180.0631-0.3452-0.13020.14410.2914-0.0620.08372.21120.02770.23431.08630.23480.5957353.9417158.7134112.3456
550.5217-1.579-0.21514.88050.66890.07910.0459-0.2830.07740.2665-0.1581-0.59860.25510.12270.07980.80530.0001-0.11540.6747-0.14490.9171379.3822127.0165200.9897
560.4968-0.66840.05582.5855-1.09261.2467-0.3578-0.0377-0.09660.13910.3145-0.2746-0.14990.78320.2180.40650.1704-0.04470.56390.00230.5447356.1698144.3222174.0326
571.2126-0.4065-0.38492.1089-0.32921.0691-0.2215-0.0063-0.031-0.43080.3419-0.1565-0.10230.35020.06120.5131-0.00060.04090.32190.07910.6909347.7871143.9548160.8526
581.2253-0.480.4431.2554-0.1981.17050.05680.18550.1643-0.1916-0.0399-0.2457-0.16190.16960.00990.4282-0.04940.1520.26940.00160.6911370.4761121.9668169.7218
591.639-2.46330.07053.7769-0.080.012-0.18980.07630.37220.0798-0.07490.0227-0.4825-0.3430.05551.29990.13870.19551.09390.08561.0629336.636140.8982193.1208
601.13920.05640.82340.73830.14120.61160.45680.05630.68040.00490.25640.0681-0.547-0.176-0.62550.81750.03370.14560.6818-0.18430.8486331.432293.9133162.0798
611.9444-0.0327-0.33061.0399-0.30741.8701-0.04470.216-0.1482-0.6512-0.13410.03020.11260.06820.01730.70850.02320.15020.3901-0.0270.6969359.7917129.9943148.5018
621.20080.2954-0.26891.0553-0.02961.4202-0.00070.07730.1269-0.22890.10490.2292-0.1862-0.20740.04190.44730.09380.05270.30690.07060.7399335.6005122.6199171.7075
630.7606-0.3874-1.170.19890.59831.7877-0.02320.2101-0.0961-0.0660.0439-0.0204-0.03590.0451-0.00241.27150.13520.17660.67650.04651.2295368.5171102.3629155.4479
641.48470.2576-0.13930.9119-0.36861.20430.14750.14720.0978-0.0072-0.0490.1864-0.2595-0.2421-0.06440.39590.0137-0.08890.46390.03280.2925336.141464.6338141.3811
650.8682-0.0016-0.02710.61330.24941.09290.15160.7330.2715-0.5667-0.0577-0.1102-0.4215-0.11690.09640.77160.1064-0.00010.89770.19010.313345.997577.1684112.6726
661.0419-0.15960.16821.5588-0.32971.20250.00420.34580.1112-0.1290.032-0.3918-0.17630.2293-0.02170.3994-0.03420.08470.5218-0.01070.3042369.427469.9427135.9253
670.9659-0.00950.4060.64190.02991.11540.13030.2019-0.3331-0.01220.0202-0.0510.39560.0461-0.06310.48730.0317-0.1220.3861-0.09170.4373360.106240.2864146.8182
681.4350.2087-1.08031.4321-0.89381.19360.27990.1389-0.1145-0.23880.3966-0.22960.08690.3514-0.28730.92050.00520.17930.65620.12021.0047374.3061122.6288158.7801
691.51150.58660.67980.61730.60041.38270.02030.23540.015-0.21090.0855-0.21680.01120.14140.05870.41730.02260.06640.2481-0.02160.5231360.925494.3036161.5936
703.4834-0.45520.29366.15580.02424.16930.0740.17610.0310.0221-0.08240.37340.0483-0.15750.03440.50930.1386-0.00680.49460.17940.6105331.618785.8321201.5697
710.7136-0.7003-0.18082.28891.86341.7995-0.35620.07560.12560.21640.25160.41570.3623-0.63080.05070.54890.16270.07390.55540.06760.3509354.294475.6614169.1342
721.7982-0.15040.20732.6040.0251.56610.19340.18850.0508-0.02930.10520.0894-0.0551-0.1755-0.03120.37820.0179-0.02620.3315-0.05940.4366359.278574.2851160.6647
731.2912-0.2687-0.18671.335-0.00420.9758-0.02360.0825-0.0024-0.02690.06530.21320.0432-0.14510.03150.2962-0.01320.0220.2755-0.01460.5727340.195194.2958172.648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 315 )A84 - 315
2X-RAY DIFFRACTION2chain 'A' and (resid 316 through 687 )A316 - 687
3X-RAY DIFFRACTION3chain 'B' and (resid 81 through 277 )B81 - 277
4X-RAY DIFFRACTION4chain 'B' and (resid 278 through 687 )B278 - 687
5X-RAY DIFFRACTION5chain 'C' and (resid 42 through 76 )C42 - 76
6X-RAY DIFFRACTION6chain 'C' and (resid 77 through 155 )C77 - 155
7X-RAY DIFFRACTION7chain 'C' and (resid 156 through 294 )C156 - 294
8X-RAY DIFFRACTION8chain 'D' and (resid 43 through 76 )D43 - 76
9X-RAY DIFFRACTION9chain 'D' and (resid 77 through 155 )D77 - 155
10X-RAY DIFFRACTION10chain 'D' and (resid 156 through 292 )D156 - 292
11X-RAY DIFFRACTION11chain 'E' and (resid 85 through 296 )E85 - 296
12X-RAY DIFFRACTION12chain 'E' and (resid 297 through 687 )E297 - 687
13X-RAY DIFFRACTION13chain 'F' and (resid 84 through 278 )F84 - 278
14X-RAY DIFFRACTION14chain 'F' and (resid 279 through 687 )F279 - 687
15X-RAY DIFFRACTION15chain 'G' and (resid 43 through 77 )G43 - 77
16X-RAY DIFFRACTION16chain 'G' and (resid 78 through 295 )G78 - 295
17X-RAY DIFFRACTION17chain 'H' and (resid 42 through 55 )H42 - 55
18X-RAY DIFFRACTION18chain 'H' and (resid 56 through 77 )H56 - 77
19X-RAY DIFFRACTION19chain 'H' and (resid 78 through 293 )H78 - 293
20X-RAY DIFFRACTION20chain 'I' and (resid 84 through 265 )I84 - 265
21X-RAY DIFFRACTION21chain 'I' and (resid 266 through 343 )I266 - 343
22X-RAY DIFFRACTION22chain 'I' and (resid 344 through 687 )I344 - 687
23X-RAY DIFFRACTION23chain 'J' and (resid 84 through 457 )J84 - 457
24X-RAY DIFFRACTION24chain 'J' and (resid 458 through 685 )J458 - 685
25X-RAY DIFFRACTION25chain 'K' and (resid 42 through 66 )K42 - 66
26X-RAY DIFFRACTION26chain 'K' and (resid 67 through 99 )K67 - 99
27X-RAY DIFFRACTION27chain 'K' and (resid 100 through 275 )K100 - 275
28X-RAY DIFFRACTION28chain 'K' and (resid 276 through 295 )K276 - 295
29X-RAY DIFFRACTION29chain 'L' and (resid 41 through 55 )L41 - 55
30X-RAY DIFFRACTION30chain 'L' and (resid 56 through 89 )L56 - 89
31X-RAY DIFFRACTION31chain 'L' and (resid 90 through 155 )L90 - 155
32X-RAY DIFFRACTION32chain 'L' and (resid 156 through 279 )L156 - 279
33X-RAY DIFFRACTION33chain 'L' and (resid 280 through 295 )L280 - 295
34X-RAY DIFFRACTION34chain 'M' and (resid 83 through 296 )M83 - 296
35X-RAY DIFFRACTION35chain 'M' and (resid 297 through 687 )M297 - 687
36X-RAY DIFFRACTION36chain 'N' and (resid 85 through 255 )N85 - 255
37X-RAY DIFFRACTION37chain 'N' and (resid 256 through 296 )N256 - 296
38X-RAY DIFFRACTION38chain 'N' and (resid 297 through 654 )N297 - 654
39X-RAY DIFFRACTION39chain 'N' and (resid 655 through 687 )N655 - 687
40X-RAY DIFFRACTION40chain 'O' and (resid 50 through 66 )O50 - 66
41X-RAY DIFFRACTION41chain 'O' and (resid 67 through 89 )O67 - 89
42X-RAY DIFFRACTION42chain 'O' and (resid 90 through 155 )O90 - 155
43X-RAY DIFFRACTION43chain 'O' and (resid 156 through 279 )O156 - 279
44X-RAY DIFFRACTION44chain 'O' and (resid 280 through 293 )O280 - 293
45X-RAY DIFFRACTION45chain 'P' and (resid 42 through 55 )P42 - 55
46X-RAY DIFFRACTION46chain 'P' and (resid 56 through 84 )P56 - 84
47X-RAY DIFFRACTION47chain 'P' and (resid 85 through 140 )P85 - 140
48X-RAY DIFFRACTION48chain 'P' and (resid 141 through 294 )P141 - 294
49X-RAY DIFFRACTION49chain 'Q' and (resid 84 through 366 )Q84 - 366
50X-RAY DIFFRACTION50chain 'Q' and (resid 367 through 687 )Q367 - 687
51X-RAY DIFFRACTION51chain 'R' and (resid 84 through 255 )R84 - 255
52X-RAY DIFFRACTION52chain 'R' and (resid 256 through 407 )R256 - 407
53X-RAY DIFFRACTION53chain 'R' and (resid 408 through 544 )R408 - 544
54X-RAY DIFFRACTION54chain 'R' and (resid 545 through 650 )R545 - 650
55X-RAY DIFFRACTION55chain 'S' and (resid 43 through 66 )S43 - 66
56X-RAY DIFFRACTION56chain 'S' and (resid 67 through 85 )S67 - 85
57X-RAY DIFFRACTION57chain 'S' and (resid 86 through 150 )S86 - 150
58X-RAY DIFFRACTION58chain 'S' and (resid 151 through 280 )S151 - 280
59X-RAY DIFFRACTION59chain 'S' and (resid 281 through 295 )S281 - 295
60X-RAY DIFFRACTION60chain 'T' and (resid 45 through 77 )T45 - 77
61X-RAY DIFFRACTION61chain 'T' and (resid 78 through 155 )T78 - 155
62X-RAY DIFFRACTION62chain 'T' and (resid 156 through 279 )T156 - 279
63X-RAY DIFFRACTION63chain 'T' and (resid 280 through 291 )T280 - 291
64X-RAY DIFFRACTION64chain 'U' and (resid 84 through 283 )U84 - 283
65X-RAY DIFFRACTION65chain 'U' and (resid 284 through 687 )U284 - 687
66X-RAY DIFFRACTION66chain 'V' and (resid 83 through 277 )V83 - 277
67X-RAY DIFFRACTION67chain 'V' and (resid 278 through 687 )V278 - 687
68X-RAY DIFFRACTION68chain 'W' and (resid 44 through 76 )W44 - 76
69X-RAY DIFFRACTION69chain 'W' and (resid 77 through 292 )W77 - 292
70X-RAY DIFFRACTION70chain 'X' and (resid 49 through 66 )X49 - 66
71X-RAY DIFFRACTION71chain 'X' and (resid 67 through 89 )X67 - 89
72X-RAY DIFFRACTION72chain 'X' and (resid 90 through 150 )X90 - 150
73X-RAY DIFFRACTION73chain 'X' and (resid 151 through 296 )X151 - 296

+
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