[English] 日本語
Yorodumi
- PDB-2jfd: Structure of the MAT domain of human FAS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jfd
TitleStructure of the MAT domain of human FAS
ComponentsFATTY ACID SYNTHASE
KeywordsTRANSFERASE / OXIDOREDUCTASE / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / ether lipid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity ...fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / ether lipid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / glandular epithelial cell development / : / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / Fatty acyl-CoA biosynthesis / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / modulation by host of viral process / ChREBP activates metabolic gene expression / [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 / fatty acid synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / phosphopantetheine binding / monocyte differentiation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / osteoblast differentiation / fatty acid biosynthetic process / melanosome / cadherin binding / inflammatory response / Golgi apparatus / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3290 / : / Fatty acid synthase, pseudo-KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : ...Alpha-Beta Plaits - #3290 / : / Fatty acid synthase, pseudo-KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / Thioesterase / Thioesterase domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / GroES-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsBunkoczi, G. / Kavanagh, K. / Hozjan, V. / Rojkova, A. / Wu, X. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Smith, S. / Oppermann, U.
CitationJournal: Chem. Biol. / Year: 2009
Title: Structural basis for different specificities of acyltransferases associated with the human cytosolic and mitochondrial fatty acid synthases.
Authors: Bunkoczi, G. / Misquitta, S. / Wu, X. / Lee, W.H. / Rojkova, A. / Kochan, G. / Kavanagh, K.L. / Oppermann, U. / Smith, S.
History
DepositionJan 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references / Derived calculations
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_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
B: FATTY ACID SYNTHASE
C: FATTY ACID SYNTHASE
D: FATTY ACID SYNTHASE


Theoretical massNumber of molelcules
Total (without water)186,9474
Polymers186,9474
Non-polymers00
Water27015
1
A: FATTY ACID SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,7371
Polymers46,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FATTY ACID SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,7371
Polymers46,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FATTY ACID SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,7371
Polymers46,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FATTY ACID SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,7371
Polymers46,7371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.980, 92.690, 259.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13B
23C
14A
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETSERSER2AA421 - 42723 - 29
211METMETSERSER2BB421 - 42723 - 29
311METMETSERSER2CC421 - 42723 - 29
411METMETSERSER2DD421 - 42723 - 29
121GLNGLNPROPRO2AA440 - 48642 - 88
221GLNGLNPROPRO2BB440 - 48642 - 88
321GLNGLNPROPRO2CC440 - 48642 - 88
421GLNGLNPROPRO2DD440 - 48642 - 88
131ARGARGSERSER2AA490 - 49792 - 99
231ARGARGSERSER2BB490 - 49792 - 99
331ARGARGSERSER2CC490 - 49792 - 99
431ARGARGSERSER2DD490 - 49792 - 99
141GLNGLNPROPRO2AA502 - 654104 - 256
241GLNGLNPROPRO2BB502 - 654104 - 256
341GLNGLNPROPRO2CC502 - 654104 - 256
441GLNGLNPROPRO2DD502 - 654104 - 256
151GLNGLNTHRTHR5AA655 - 677257 - 279
251GLNGLNTHRTHR5BB655 - 677257 - 279
351GLNGLNTHRTHR5CC655 - 677257 - 279
451GLNGLNTHRTHR5DD655 - 677257 - 279
161GLYGLYGLUGLU2AA678 - 719280 - 321
261GLYGLYGLUGLU2BB678 - 719280 - 321
361GLYGLYGLUGLU2CC678 - 719280 - 321
461GLYGLYGLUGLU2DD678 - 719280 - 321
171SERSERGLYGLY2AA725 - 774327 - 376
271SERSERGLYGLY2BB725 - 774327 - 376
371SERSERGLYGLY2CC725 - 774327 - 376
471SERSERGLYGLY2DD725 - 774327 - 376
181CYSCYSPROPRO2AA779 - 818381 - 420
281CYSCYSPROPRO2BB779 - 818381 - 420
381CYSCYSPROPRO2CC779 - 818381 - 420
481CYSCYSPROPRO2DD779 - 818381 - 420
112GLYGLYGLUGLU5AA428 - 43930 - 41
212GLYGLYGLUGLU5BB428 - 43930 - 41
312GLYGLYGLUGLU5CC428 - 43930 - 41
412GLYGLYGLUGLU5DD428 - 43930 - 41
122ALAALAGLUGLU5AA487 - 48989 - 91
222ALAALAGLUGLU5BB487 - 48989 - 91
322ALAALAGLUGLU5CC487 - 48989 - 91
422ALAALAGLUGLU5DD487 - 48989 - 91
132ALAALASERSER5AA720 - 724322 - 326
232ALAALASERSER5BB720 - 724322 - 326
332ALAALASERSER5CC720 - 724322 - 326
432ALAALASERSER5DD720 - 724322 - 326
142LEULEUSERSER5AA775 - 778377 - 380
242LEULEUSERSER5BB775 - 778377 - 380
342LEULEUSERSER5CC775 - 778377 - 380
442LEULEUSERSER5DD775 - 778377 - 380
113GLYGLYTHRTHR2BB498 - 501100 - 103
213GLYGLYTHRTHR2CC498 - 501100 - 103
123VALVALPROPRO5BB819 - 822421 - 424
223VALVALPROPRO5CC819 - 822421 - 424
114GLYGLYTHRTHR2AA498 - 501100 - 103
214GLYGLYTHRTHR2DD498 - 501100 - 103

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.99661, 0.08201, 0.00652), (0.05607, 0.61912, 0.78329), (0.0602, 0.781, -0.62162)39.55054, -18.45874, 34.49465
2given(0.15098, 0.5053, 0.84963), (-0.97281, 0.22867, 0.03687), (-0.17565, -0.8321, 0.52608)-43.81604, 57.98491, -81.5965
3given(-0.22265, 0.97472, -0.01865), (0.97488, 0.22273, 0.00227), (0.00636, -0.01767, -0.99982)-17.4661, 18.16736, -54.17027

-
Components

#1: Protein
FATTY ACID SYNTHASE /


Mass: 46736.711 Da / Num. of mol.: 4 / Fragment: MAT DOMAIN, RESIDUES 422-823
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P49327, fatty-acid synthase system
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
Description: ANISOTROPIC SCALING WAS PERFORMED USING THE DIFFRACTION ANISOTROPY SERVER
Crystal growpH: 8.5 / Details: 20% PEG10K, 0.04 M NAKPO4, 25% GLYCEROL, pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→45.3 Å / Num. obs: 51294 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.39 / % possible all: 90.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→45.22 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 39.416 / SU ML: 0.347 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2074 5 %RANDOM
Rwork0.212 ---
obs0.215 39706 81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.81→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11370 0 0 15 11385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111653
X-RAY DIFFRACTIONr_bond_other_d0.0020.027442
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.96415955
X-RAY DIFFRACTIONr_angle_other_deg0.946318233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8451599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09923.351385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.006151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5341556
X-RAY DIFFRACTIONr_chiral_restr0.0670.21861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022290
X-RAY DIFFRACTIONr_nbd_refined0.2410.23333
X-RAY DIFFRACTIONr_nbd_other0.1930.27825
X-RAY DIFFRACTIONr_nbtor_refined0.1890.26008
X-RAY DIFFRACTIONr_nbtor_other0.0920.26212
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2324
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.50638114
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.202512662
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8383943
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.844113293
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2019tight positional0.040.05
12B2019tight positional0.040.05
13C2019tight positional0.050.05
14D2019tight positional0.040.05
31B22tight positional0.040.05
41A22tight positional0.030.05
11A1853medium positional0.640.5
12B1853medium positional0.540.5
13C1853medium positional0.460.5
14D1853medium positional0.530.5
21A140medium positional0.510.5
22B140medium positional0.270.5
23C140medium positional0.440.5
24D140medium positional0.290.5
31B32medium positional0.180.5
41A9medium positional0.180.5
11A60loose positional1.195
12B60loose positional0.995
13C60loose positional0.795
14D60loose positional1.415
21A117loose positional0.895
22B117loose positional0.735
23C117loose positional1.035
24D117loose positional0.735
31B31loose positional0.535
11A2019tight thermal0.792
12B2019tight thermal0.682
13C2019tight thermal0.912
14D2019tight thermal0.652
31B22tight thermal0.472
41A22tight thermal0.672
11A1853medium thermal2.525
12B1853medium thermal2.095
13C1853medium thermal2.615
14D1853medium thermal2.065
21A140medium thermal1.975
22B140medium thermal1.75
23C140medium thermal2.225
24D140medium thermal1.915
31B32medium thermal0.845
41A9medium thermal1.175
11A60loose thermal6.2710
12B60loose thermal4.1410
13C60loose thermal3.8210
14D60loose thermal2.5710
21A117loose thermal3.7410
22B117loose thermal3.4910
23C117loose thermal4.0210
24D117loose thermal3.1210
31B31loose thermal3.3510
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 33 -
Rwork0.28 865 -
obs--23.88 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.65970.9401-1.20963.0121-0.64516.2895-0.12330.10180.198-0.06660.14480.15890.2607-0.3548-0.02150.06690.0789-0.079-0.16920.1048-0.08325.926922.201441.5854
21.2915-0.3517-0.37783.7726-0.97893.4593-0.0575-0.39770.00670.2630.60120.6335-0.3622-0.6988-0.5437-0.30310.12110.00960.22710.21390.101213.01716.4963.4508
34.85360.5304-1.28681.1349-1.96626.2621-0.2370.0210.1225-0.02390.2305-0.01810.308-0.26060.0065-0.0931-0.03510.0426-0.42820.0495-0.212730.6215-11.421973.6014
41.63620.2996-1.75333.3871-1.73753.88210.7387-0.4168-0.1542-0.23350.09350.59370.4176-1.0213-0.8323-0.2787-0.18270.02910.1730.26670.078313.778-9.377573.8647
50.5994-0.0010.17413.7441-1.75311.7082-0.0217-0.0681-0.0905-0.44620.37110.47730.1673-0.6243-0.3494-0.0482-0.1027-0.12950.01910.1236-0.060620.17921.164154.539
63.4805-0.6059-0.87791.1316-0.70696.50830.13-1.0930.04080.5343-0.17760.30970.1037-1.01870.04760.2054-0.0353-0.13930.25040.0998-0.035616.260828.98227.8241
72.42670.0870.88664.35811.10048.9148-0.04410.5152-0.1222-0.238-0.1514-0.2304-1.13151.34280.1955-0.0364-0.1478-0.23590.17940.1463-0.158127.559736.27850.9705
84.4444-0.74473.12512.6882.126710.31490.42742.07450.1052-0.7447-0.35570.82790.0052-1.282-0.07160.25270.0938-0.27560.63180.0660.00129.560633.61-18.6394
920.19-3.2997-1.96285.50420.28665.67660.06681.29790.4092-1.1522-0.233-0.6269-0.18091.02190.16610.44410.0954-0.10460.5598-0.0115-0.418226.472433.9309-17.8715
102.63820.23232.45061.31120.15919.60630.07980.2253-0.335-0.157-0.0650.05630.5494-0.0681-0.0148-0.0810.0027-0.148-0.12270.0448-0.026820.400826.34293.4276
113.14741.9952-0.91075.9908-1.85115.69240.16740.3726-0.2328-0.23280.1140.01250.55780.0027-0.28130.10730.12320.0203-0.2531-0.0456-0.11656.689839.3968-82.9098
121.55020.9727-0.3982.24740.29055.04190.2403-0.0888-0.01990.0606-0.1643-0.3646-0.63060.7352-0.0761-0.085-0.1182-0.0802-0.24350.0491-0.105415.176149.4923-56.2815
131.1565-1.4173-0.2785.81121.22527.4634-0.7205-0.1399-0.10780.18050.75680.01321.12362.0857-0.03620.19810.214-0.1410.2660.0113-0.193617.651929.4964-38.7303
142.0568-1.3629-1.90831.3753.261710.222-0.4302-0.77810.30370.26320.7603-0.76580.19381.3973-0.33010.2095-0.3307-0.1910.0132-0.0239-0.193916.065845.7011-37.3357
151.17960.5215-0.76720.6098-0.38144.83130.19970.0291-0.06550.0616-0.1452-0.24030.22350.1551-0.0545-0.04110.0375-0.1014-0.3726-0.0182-0.14456.066841.4464-57.5244
162.07330.68-0.83440.84480.53156.66340.25290.2028-0.218-0.2532-0.29020.17890.030.10610.03730.07530.023-0.0094-0.2223-0.0349-0.0919-2.005948.1175-95.7535
172.04192.09862.03112.15842.1837.49490.47720.3399-0.2112-0.4327-0.14870.2639-0.0326-0.1806-0.32850.51420.0959-0.16380.0257-0.260.1641-14.767932.4008-117.3013
186.5157-4.118-0.38092.8013-0.60823.65061.03890.41360.23010.14240.05010.48270.1285-0.8034-1.08910.8396-0.0063-0.1690.6136-0.35240.8105-36.746344.4393-128.189
194.206-0.75530.09345.98361.77410.55050.00420.8651-0.0369-1.1020.20290.95430.4143-0.2914-0.20710.73650.0305-0.41670.304-0.32920.4089-30.513528.9547-127.4183
201.07011.25151.70121.84541.58373.13580.19820.03570.0492-0.2096-0.58860.78240.1722-0.68210.39050.3949-0.0527-0.14410.1768-0.29340.3381-21.617438.1372-108.5894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A419 - 489
2X-RAY DIFFRACTION2A490 - 606
3X-RAY DIFFRACTION3A607 - 673
4X-RAY DIFFRACTION4A674 - 703
5X-RAY DIFFRACTION5A704 - 822
6X-RAY DIFFRACTION6B420 - 489
7X-RAY DIFFRACTION7B490 - 606
8X-RAY DIFFRACTION8B607 - 673
9X-RAY DIFFRACTION9B674 - 703
10X-RAY DIFFRACTION10B704 - 822
11X-RAY DIFFRACTION11C420 - 489
12X-RAY DIFFRACTION12C490 - 606
13X-RAY DIFFRACTION13C607 - 673
14X-RAY DIFFRACTION14C674 - 703
15X-RAY DIFFRACTION15C704 - 822
16X-RAY DIFFRACTION16D419 - 489
17X-RAY DIFFRACTION17D490 - 606
18X-RAY DIFFRACTION18D607 - 673
19X-RAY DIFFRACTION19D674 - 703
20X-RAY DIFFRACTION20D704 - 819

+
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