[English] 日本語
Yorodumi
- PDB-6ql9: Structure of Fatty acid synthase complex from Saccharomyces cerev... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ql9
TitleStructure of Fatty acid synthase complex from Saccharomyces cerevisiae at 2.9 Angstrom
Components(Fatty acid synthase subunit ...) x 3
KeywordsTRANSFERASE / Fatty acid synthase / Acyl carrier protein / Ketosynthase / Ketoreductase / Enoyl reductase / Dehydratase / Malonyl/palmitoyl transferase / Acetyl transferase / Phosphopantetheine transferase
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
: / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast ...: / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-2'-5'-DIPHOSPHATE / ACETATE ION / FLAVIN MONONUCLEOTIDE / MALONATE ION / TRIETHYLENE GLYCOL / 4'-PHOSPHOPANTETHEINE / Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsSingh, K. / Graf, B. / Linden, A. / Sautner, V. / Urlaub, H. / Tittmann, K. / Stark, H. / Chari, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860-TP A5 Germany
CitationJournal: Cell / Year: 2020
Title: Discovery of a Regulatory Subunit of the Yeast Fatty Acid Synthase.
Authors: Kashish Singh / Benjamin Graf / Andreas Linden / Viktor Sautner / Henning Urlaub / Kai Tittmann / Holger Stark / Ashwin Chari /
Abstract: Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid ...Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid synthesis, the growing fatty acid chain is thought to be shuttled by the dynamic acyl carrier protein domain to several enzyme active sites. Here, we report the discovery of a γ subunit of the 2.6 megadalton α-βS. cerevisiae FAS, which is shown by high-resolution structures to stabilize a rotated FAS conformation and rearrange ACP domains from equatorial to axial positions. The γ subunit spans the length of the FAS inner cavity, impeding reductase activities of FAS, regulating NADPH turnover by kinetic hysteresis at the ketoreductase, and suppressing off-pathway reactions at the enoylreductase. The γ subunit delineates the functional compartment within FAS. As a scaffold, it may be exploited to incorporate natural and designed enzymatic activities that are not present in natural FAS.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit alpha
C: Fatty acid synthase subunit alpha
D: Fatty acid synthase subunit alpha
E: Fatty acid synthase subunit alpha
F: Fatty acid synthase subunit alpha
G: Fatty acid synthase subunit beta
H: Fatty acid synthase subunit beta
I: Fatty acid synthase subunit beta
J: Fatty acid synthase subunit beta
K: Fatty acid synthase subunit beta
L: Fatty acid synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,630,308145
Polymers2,617,09312
Non-polymers13,215133
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area204330 Å2
ΔGint-1113 kcal/mol
Surface area859010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.616, 347.596, 265.266
Angle α, β, γ (deg.)90.00, 107.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F
116G
216H
117G
217I
118G
218J
119G
219K
120G
220L
121H
221I
122H
222J
123H
223K
124H
224L
125I
225J
126I
226K
127I
227L
128J
228K
129J
229L
130K
230L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 18861 - 1886
21METMETLYSLYSBB1 - 18861 - 1886
12METMETLYSLYSAA1 - 18861 - 1886
22METMETLYSLYSCC1 - 18861 - 1886
13METMETLYSLYSAA1 - 18861 - 1886
23METMETLYSLYSDD1 - 18861 - 1886
14METMETLYSLYSAA1 - 18861 - 1886
24METMETLYSLYSEE1 - 18861 - 1886
15METMETLYSLYSAA1 - 18861 - 1886
25METMETLYSLYSFF1 - 18861 - 1886
16METMETLYSLYSBB1 - 18861 - 1886
26METMETLYSLYSCC1 - 18861 - 1886
17METMETLYSLYSBB1 - 18861 - 1886
27METMETLYSLYSDD1 - 18861 - 1886
18METMETLYSLYSBB1 - 18861 - 1886
28METMETLYSLYSEE1 - 18861 - 1886
19METMETLYSLYSBB1 - 18861 - 1886
29METMETLYSLYSFF1 - 18861 - 1886
110METMETLYSLYSCC1 - 18861 - 1886
210METMETLYSLYSDD1 - 18861 - 1886
111METMETLYSLYSCC1 - 18861 - 1886
211METMETLYSLYSEE1 - 18861 - 1886
112METMETLYSLYSCC1 - 18861 - 1886
212METMETLYSLYSFF1 - 18861 - 1886
113METMETLYSLYSDD1 - 18861 - 1886
213METMETLYSLYSEE1 - 18861 - 1886
114METMETLYSLYSDD1 - 18861 - 1886
214METMETLYSLYSFF1 - 18861 - 1886
115METMETLYSLYSEE1 - 18861 - 1886
215METMETLYSLYSFF1 - 18861 - 1886
116SERSERGLNGLNGG5 - 20505 - 2050
216SERSERGLNGLNHH5 - 20505 - 2050
117SERSERGLNGLNGG5 - 20505 - 2050
217SERSERGLNGLNII5 - 20505 - 2050
118SERSERGLNGLNGG5 - 20505 - 2050
218SERSERGLNGLNJJ5 - 20505 - 2050
119SERSERGLNGLNGG5 - 20505 - 2050
219SERSERGLNGLNKK5 - 20505 - 2050
120SERSERGLNGLNGG5 - 20505 - 2050
220SERSERGLNGLNLL5 - 20505 - 2050
121SERSERGLUGLUHH5 - 20495 - 2049
221SERSERGLUGLUII5 - 20495 - 2049
122TYRTYRGLNGLNHH4 - 20504 - 2050
222TYRTYRGLNGLNJJ4 - 20504 - 2050
123TYRTYRGLNGLNHH4 - 20504 - 2050
223TYRTYRGLNGLNKK4 - 20504 - 2050
124TYRTYRGLNGLNHH4 - 20504 - 2050
224TYRTYRGLNGLNLL4 - 20504 - 2050
125SERSERGLUGLUII5 - 20495 - 2049
225SERSERGLUGLUJJ5 - 20495 - 2049
126SERSERGLUGLUII5 - 20495 - 2049
226SERSERGLUGLUKK5 - 20495 - 2049
127SERSERGLNGLNII5 - 20505 - 2050
227SERSERGLNGLNLL5 - 20505 - 2050
128TYRTYRGLNGLNJJ4 - 20504 - 2050
228TYRTYRGLNGLNKK4 - 20504 - 2050
129TYRTYRGLNGLNJJ4 - 20504 - 2050
229TYRTYRGLNGLNLL4 - 20504 - 2050
130TYRTYRGLNGLNKK4 - 20504 - 2050
230TYRTYRGLNGLNLL4 - 20504 - 2050

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

-
Components

-
Fatty acid synthase subunit ... , 3 types, 12 molecules ABCDEFGJHIKL

#1: Protein
Fatty acid synthase subunit alpha /


Mass: 207184.422 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P19097, fatty-acyl-CoA synthase system, 3-oxoacyl-[acyl-carrier-protein] reductase, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Fatty acid synthase subunit beta /


Mass: 228940.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S- ...References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase
#3: Protein
Fatty acid synthase subunit beta /


Mass: 229026.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S- ...References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase

-
Non-polymers , 9 types, 461 molecules

#4: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: C2H6O2 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#6: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: Na / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#7: Chemical
ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H3O2 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#10: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#11: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H2O4 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M hepes pH 7.0, 0.3 M sodium-malonate pH 7.0 , 11.5-13% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2018 / Details: CRL Transfocator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.82→191.5 Å / Num. obs: 894158 / % possible obs: 96.5 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rpim(I) all: 0.07272 / Net I/σ(I): 10.91
Reflection shellResolution: 2.82→2.9 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 4914 / CC1/2: 0.241 / Rpim(I) all: 1.096 / % possible all: 76.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.3data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UV8

2uv8


Resolution: 2.82→191.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.928 / SU B: 35.08 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21135 35171 5 %RANDOM
Rwork0.19248 ---
obs0.19342 671162 78.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å2-0.98 Å2
2---0.23 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.82→191.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms178375 0 703 328 179406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013182757
X-RAY DIFFRACTIONr_bond_other_d0.0010.017170733
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.645247451
X-RAY DIFFRACTIONr_angle_other_deg1.2241.576397551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.996522746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75523.558870
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.311532054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.38915822
X-RAY DIFFRACTIONr_chiral_restr0.0640.224087
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02202822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0236306
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_it1.253.07791080
X-RAY DIFFRACTIONr_mcbond_other1.2493.07791073
X-RAY DIFFRACTIONr_mcangle_it2.1434.614113787
X-RAY DIFFRACTIONr_mcangle_other2.1434.614113788
X-RAY DIFFRACTIONr_scbond_it1.3113.20391677
X-RAY DIFFRACTIONr_scbond_other1.3113.20391678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2454.749133664
X-RAY DIFFRACTIONr_long_range_B_refined4.3335.708200133
X-RAY DIFFRACTIONr_long_range_B_other4.3335.708200134
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: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A567410.06
12B567410.06
21A567620.05
22C567620.05
31A567410.05
32D567410.05
41A566910.05
42E566910.05
51A566280.06
52F566280.06
61B567580.05
62C567580.05
71B567580.06
72D567580.06
81B567520.06
82E567520.06
91B567560.06
92F567560.06
101C567280.05
102D567280.05
111C567250.05
112E567250.05
121C566840.05
122F566840.05
131D566280.06
132E566280.06
141D566660.06
142F566660.06
151E566050.06
152F566050.06
161G659230.06
162H659230.06
171G658660.06
172I658660.06
181G659190.06
182J659190.06
191G656470.06
192K656470.06
201G657620.06
202L657620.06
211H660450.06
212I660450.06
221H660890.06
222J660890.06
231H659280.06
232K659280.06
241H659010.06
242L659010.06
251I660580.05
252J660580.05
261I660330.05
262K660330.05
271I659520.06
272L659520.06
281J658020.06
282K658020.06
291J658710.06
292L658710.06
301K656670.06
302L656670.06
LS refinement shellResolution: 2.819→2.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 121 -
Rwork0.352 2172 -
obs--3.46 %
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)
11.2416-0.1247-1.03921.7150.03361.85990.23150.32850.1487-0.53040.0691-0.0717-0.4895-0.1502-0.30060.75390.06720.14520.4977-0.01120.5505104.880660.36698.9802
20.37790.1232-0.1871.7503-1.42071.29120.03390.30330.0322-0.5329-0.121-0.35280.24090.13160.08710.69950.03060.06460.6655-0.08640.827556.196136.559536.9624
30.475-0.58550.17931.0189-0.20150.2894-0.0341-0.02780.2305-0.0589-0.0008-0.3073-0.09220.26750.03490.0825-0.02890.02320.4889-0.08660.2947117.348725.837781.3928
40.95880.07510.1480.56120.05510.6466-0.0323-0.0891-0.0674-0.05390.0306-0.04070.08430.18560.00160.03820.07710.04650.32090.05750.1113108.2983-24.379272.7523
51.7824-1.05710.51525.6863-1.850.71170.27460.1456-0.13550.0912-0.3605-0.75070.12440.37310.0860.63480.25860.00841.23640.10560.8573150.3372-51.627776.9156
61.3263-0.6782-0.28211.29250.55181.71450.0230.09640.0998-0.29390.0757-0.0479-0.13190.2373-0.09870.3279-0.00840.03190.5935-0.0030.392286.5518-70.966210.8297
71.7534-0.6586-0.74710.8420.55950.68980.13610.523-0.1628-0.4456-0.0387-0.0918-0.00220.128-0.09740.62860.0501-0.05360.78080.02120.727768.8198-24.084645.6279
81.2447-0.05170.33510.2834-0.0980.4756-0.0110.1224-0.4258-0.05780.01580.06660.27080.0057-0.00480.23480.05150.15170.15690.0440.404316.6976-79.751651.4096
90.7040.02470.0510.78560.05130.6264-0.04420.0766-0.1265-0.0433-0.02140.02150.1052-0.04630.06560.0547-0.01970.08790.0481-0.05330.1961-14.8364-45.355329.0789
107.410.8881.43631.91230.49482.0349-0.17140.3239-0.8175-0.15350.06360.41780.6839-0.27870.10780.6236-0.07680.08070.5518-0.17790.7237-51.5588-67.49853.1525
111.21360.19340.52290.8047-0.25762.8558-0.02820.3162-0.106-0.2128-0.0609-0.05170.25970.24470.08910.6925-0.05010.16640.4243-0.06920.5522-12.02479.8111-30.6258
120.49030.45460.69421.12141.07461.4411-0.16450.43940.1159-0.49120.1071-0.2052-0.19430.31050.05740.5969-0.09590.08160.67690.04590.763112.8155-6.577724.1297
130.55160.5074-0.03411.33070.16230.317-0.04060.21370.1916-0.29640.0250.1535-0.1817-0.12820.01560.18750.0887-0.00410.16390.01860.25-16.923463.509230.0569
140.8449-0.12310.0730.6799-0.0870.56770.01170.08050.2116-0.12230.0069-0.0698-0.12720.0556-0.01860.1577-0.00780.03620.0265-0.00620.245632.104477.995938.1277
151.57351.5361.15314.6331-0.59862.0067-0.39040.01170.5372-0.46660.12820.2034-0.601-0.07290.26220.9055-0.04250.08430.53250.15421.158840.1322125.503324.1017
160.96120.3686-0.24610.4639-0.31411.7591-0.0535-0.1801-0.09430.29530.02970.0765-0.088-0.28620.02380.52620.15080.15820.81990.05930.651-10.3652-66.1136111.7225
172.43080.9921-0.7030.702-0.33710.35910.1556-0.7129-0.1460.4651-0.12340.0099-0.0003-0.0754-0.03210.65470.0232-0.02670.81630.00660.70427.1659-22.551871.4463
181.11550.0810.36750.3530.10270.54580.0077-0.2764-0.33050.1652-0.0012-0.04740.28520.049-0.00650.25650.12240.12440.24790.10760.39559.4405-78.45372.0709
190.6394-0.02620.09770.7615-0.06750.5337-0.018-0.2076-0.09820.08540.0040.02030.09340.1080.0140.07120.11410.0740.33440.10460.171791.2866-41.627490.1389
206.24520.45871.66142.5982-1.23111.98630.0948-0.256-0.53860.1810.0294-0.39250.37110.191-0.12410.53020.1843-0.03920.73890.12140.5211128.6136-61.0129117.5572
211.3098-0.03490.50260.77590.21122.41960.0683-0.4689-0.08970.2549-0.08640.11970.3510.11940.01810.63150.16950.08581.01980.01490.637888.222120.3312141.8564
220.548-0.36050.87130.5861-0.95992.2775-0.1686-0.50610.16430.43670.12760.1214-0.2973-0.27670.0410.6290.13290.03760.8413-0.07040.839163.6854-2.440290.7426
230.6151-0.36010.10141.1402-0.19490.3549-0.0598-0.23990.2720.23080.0589-0.1807-0.22040.15920.00090.1643-0.09280.00270.3597-0.14370.402593.699366.447475.1412
240.81430.03260.06750.68490.03280.6119-0.0024-0.16930.320.08210.0269-0.05-0.23550.0085-0.02450.1704-0.03470.01910.1453-0.09690.335443.917585.549165.7376
252.2169-1.41180.40182.1915-0.90010.8054-0.1050.28360.7826-0.21570.07110.1807-0.2948-0.30590.03380.8721-0.0068-0.08140.98330.15681.121193.5869-19.6575-46.8538
261.73830.7846-0.45461.8685-0.57652.0004-0.04780.33330.0928-0.31080.07430.1508-0.055-0.1254-0.02650.3538-0.06180.07450.5856-0.05510.383199.3046-50.2468-36.0444
270.3310.30450.44120.35480.45190.70150.03610.055-0.0475-0.0489-0.0480.01190.0976-0.15890.01190.2856-0.02890.13190.5307-0.0450.3746123.101-33.0886-2.237
280.2083-0.1453-0.09750.3148-0.00420.22460.04170.03620.1352-0.18030.0102-0.1379-0.13810.0673-0.05180.3061-0.0790.07280.5172-0.0410.46127.973622.57635.3691
291.22580.47650.6931.336-0.50362.6696-0.04290.06270.5009-0.1828-0.02090.3253-1.0625-0.29040.06380.85790.05290.13070.5393-0.0110.6398104.015971.763519.1727
301.678-0.5726-1.03940.22970.3550.6480.1066-0.2446-0.00440.004-0.0601-0.0501-0.04210.1753-0.04640.7837-0.11710.01250.7597-0.10690.76620.130753.392583.4402
310.73570.4726-0.07790.82180.16220.3614-0.02040.00130.1895-0.0264-0.03890.2212-0.1101-0.21040.05930.090.0690.00060.1507-0.02230.1654-35.465318.316229.5453
320.2748-0.0647-0.02950.7342-0.21420.3113-0.056-0.10550.06720.16380.04280.055-0.1003-0.0680.01320.06430.02150.01370.1542-0.09770.1243-27.9522-0.42346.5449
330.68-0.12990.16550.65240.16290.7581-0.0433-0.0163-0.17780.0121-0.02530.12780.1676-0.170.06860.0582-0.03660.05370.1441-0.09090.1861-39.3028-32.07537.9138
342.1531.77390.39756.45470.58770.24870.1347-0.0640.02-0.0225-0.16780.58010.1709-0.39040.03320.5886-0.18320.14560.9756-0.13840.8652-73.3158-53.542842.3791
351.7192-0.3711-0.27650.69590.16210.8276-0.02770.02480.25830.22770.0053-0.4976-0.3270.42610.02240.8166-0.14490.0650.6927-0.03710.581441.6257-4.9294-64.0022
360.2387-0.0628-0.00821.755-0.8690.7840.05650.10780.060.05660.00120.1056-0.32770.0077-0.05770.4234-0.04610.09380.445-0.13430.272218.2599-29.7617-51.4034
370.6415-0.0525-0.21620.2293-0.11480.70470.02240.2046-0.0026-0.0547-0.0203-0.0127-0.04540.0171-0.0020.2776-0.05250.06330.2368-0.16050.314919.6126-59.3236-30.8962
380.3383-0.00890.24280.0825-0.00051.9707-0.03090.0159-0.18970.01760.0279-0.01180.09340.13690.0030.25620.04340.10380.3476-0.01820.472464.6629-75.6721-2.2023
392.14010.0914-0.04881.6639-0.64111.18040.1538-0.2352-0.20590.3979-0.0316-0.4447-0.02170.6426-0.12220.46420.05690.08080.7476-0.01170.553996.0703-80.862223.232
400.80140.14520.53221.17910.48851.73950.13690.1499-0.52170.06390.04190.05380.2374-0.1061-0.17880.55330.01240.12520.68510.04140.738495.197729.3827-47.1364
411.6427-0.57310.06050.34470.04530.0472-0.0368-0.05790.04220.07360.057-0.0948-0.03280.0839-0.02030.79290.03380.19050.56120.12190.397175.848858.8865-36.3394
420.2298-0.0473-0.13850.15850.07930.7120.05270.11710.0435-0.13530.0176-0.0897-0.06160.1148-0.07030.68120.03330.15580.42240.11510.405641.608868.482-31.3897
431.0170.4001-1.0850.495-0.48581.5005-0.00730.14750.0131-0.2419-0.05460.0539-0.0074-0.10890.06190.57850.05940.0130.3953-0.01390.3287-1.511333.1644-33.5107
442.1267-0.0712-0.00781.39270.74091.4828-0.24660.16-0.6551-0.1510.03830.62430.5895-0.39190.20830.8382-0.05120.12840.6425-0.0940.7268-29.664.1335-28.5192
450.7352-0.11570.02131.5460.30320.96620.0035-0.21560.28790.2546-0.0866-0.5206-0.2710.4930.08310.57490.0220.06541.10410.08680.5984-19.1887-22.7589159.0767
460.7938-0.57450.60780.7875-0.68321.24630.0183-0.1074-0.12120.0542-0.096-0.03680.1910.30940.07770.28570.0430.1480.65070.02340.2982-42.6061-27.5385131.705
470.1840.0831-0.03720.430.03930.8592-0.014-0.1459-0.01090.1808-0.03480.02360.10330.09970.04890.10730.02160.07260.4443-0.04630.2843-58.4857-7.0294106.7066
480.44940.3134-0.73510.4702-0.55451.60490.0358-0.05920.09680.0783-0.04390.056-0.2462-0.08460.00810.2769-0.0104-0.02540.4051-0.10720.3675-45.279546.733396.8673
490.7601-0.32070.67631.9367-0.17982.2529-0.0804-0.0530.66770.1268-0.1335-0.1763-1.09290.48970.21381.0183-0.16760.030.6102-0.16390.767-28.646482.671987.031
501.42060.107-0.69671.0829-0.40891.4533-0.0573-0.01180.1974-0.2782-0.04180.46910.0775-0.10660.09910.7440.0544-0.04730.8326-0.12340.601734.594310.9495176.9877
510.13890.12850.0021.77390.59770.2619-0.0277-0.11790.0964-0.07860.0221-0.1339-0.06670.18650.00560.70280.21050.11230.99550.11870.377457.8776-16.2173167.6769
520.3917-0.0145-0.21840.13860.07120.6345-0.0095-0.23570.02920.17730.07440.0212-0.03970.067-0.06490.54910.23920.13020.80530.19640.382556.8383-48.3122151.4946
530.3048-0.04490.37070.1620.23542.327-0.0865-0.1698-0.21490.09430.04670.07450.0869-0.13550.03980.44560.13770.22850.63020.2050.535911.6646-68.807125.0237
542.2132-0.10190.05661.64190.69591.19630.10040.1232-0.5022-0.3466-0.17490.71680.0886-0.72270.07450.64960.10.21160.96420.09490.8953-19.8802-77.6304100.7185
550.8274-0.21990.33051.4089-0.47770.95720.0134-0.3465-0.49440.34620.0632-0.25820.44860.0191-0.07660.7948-0.0627-0.08730.8498-0.07160.6282-18.845843.66156.0455
562.10050.77210.04360.3716-0.05660.1372-0.093-0.04210.0084-0.04830.10580.02570.09280.0297-0.01280.5459-0.05080.01150.6912-0.28060.42390.527271.0697141.1458
570.218-0.0613-0.14530.2156-0.12110.5552-0.0054-0.18580.01190.0797-0.00360.03190.0406-0.02690.00910.4336-0.1062-0.01210.6953-0.29640.495734.986179.5415135.0957
580.8351-0.3954-0.96080.46390.6241.2260.0055-0.26050.01540.1125-0.0365-0.03870.01020.14890.0310.45430.0177-0.03710.9287-0.07280.474977.858243.9775141.7147
591.37950.1924-0.16481.5057-0.86031.2461-0.1645-0.335-0.54970.218-0.1095-0.6530.61490.2870.2740.84940.16410.02911.26460.04270.8407105.799914.3238140.4092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2A147 - 355
3X-RAY DIFFRACTION3A356 - 969
4X-RAY DIFFRACTION4A970 - 1778
5X-RAY DIFFRACTION5A1779 - 1887
6X-RAY DIFFRACTION6B1 - 146
7X-RAY DIFFRACTION7B147 - 355
8X-RAY DIFFRACTION8B356 - 969
9X-RAY DIFFRACTION9B970 - 1778
10X-RAY DIFFRACTION10B1779 - 1887
11X-RAY DIFFRACTION11C1 - 146
12X-RAY DIFFRACTION12C147 - 355
13X-RAY DIFFRACTION13C356 - 969
14X-RAY DIFFRACTION14C970 - 1778
15X-RAY DIFFRACTION15C1779 - 1887
16X-RAY DIFFRACTION16E1 - 146
17X-RAY DIFFRACTION17E147 - 355
18X-RAY DIFFRACTION18E356 - 969
19X-RAY DIFFRACTION19E970 - 1778
20X-RAY DIFFRACTION20E1779 - 1887
21X-RAY DIFFRACTION21F1 - 146
22X-RAY DIFFRACTION22F147 - 355
23X-RAY DIFFRACTION23F356 - 969
24X-RAY DIFFRACTION24F970 - 1778
25X-RAY DIFFRACTION24F1779 - 1887
26X-RAY DIFFRACTION25G1 - 146
27X-RAY DIFFRACTION26G147 - 355
28X-RAY DIFFRACTION27G356 - 969
29X-RAY DIFFRACTION28G970 - 1778
30X-RAY DIFFRACTION29G1779 - 1887
31X-RAY DIFFRACTION30D5 - 324
32X-RAY DIFFRACTION31D325 - 804
33X-RAY DIFFRACTION32D805 - 1292
34X-RAY DIFFRACTION33D1293 - 1772
35X-RAY DIFFRACTION34D1773 - 2048
36X-RAY DIFFRACTION35H5 - 324
37X-RAY DIFFRACTION36H325 - 804
38X-RAY DIFFRACTION37H805 - 1292
39X-RAY DIFFRACTION38H1293 - 1772
40X-RAY DIFFRACTION39H1773 - 2048
41X-RAY DIFFRACTION40I5 - 324
42X-RAY DIFFRACTION41I325 - 804
43X-RAY DIFFRACTION42I805 - 1292
44X-RAY DIFFRACTION43I1293 - 1772
45X-RAY DIFFRACTION44I1773 - 2048
46X-RAY DIFFRACTION45J5 - 324
47X-RAY DIFFRACTION46J325 - 804
48X-RAY DIFFRACTION47J805 - 1292
49X-RAY DIFFRACTION48J1293 - 1772
50X-RAY DIFFRACTION49J1773 - 2048
51X-RAY DIFFRACTION50K5 - 324
52X-RAY DIFFRACTION51K325 - 804
53X-RAY DIFFRACTION52K805 - 1292
54X-RAY DIFFRACTION53K1293 - 1772
55X-RAY DIFFRACTION54K1773 - 2048
56X-RAY DIFFRACTION55L5 - 324
57X-RAY DIFFRACTION56L325 - 804
58X-RAY DIFFRACTION57L805 - 1292
59X-RAY DIFFRACTION58L1293 - 1772
60X-RAY DIFFRACTION59L1773 - 2048

+
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