[English] 日本語
Yorodumi
- PDB-3fg6: Structure of the C-terminus of Adseverin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fg6
TitleStructure of the C-terminus of Adseverin
ComponentsAdseverin
KeywordsACTIN-BINDING PROTEIN / C-terminus of adseverin / Actin capping / Actin-binding / Cytoskeleton / Phosphoprotein
Function / homology
Function and homology information


positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping ...positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / podosome / anchoring junction / phosphatidylserine binding / brush border / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / cell projection / actin filament binding / actin cytoskeleton / actin binding / cell cortex / positive regulation of apoptotic process / negative regulation of cell population proliferation / calcium ion binding / extracellular exosome / cytoplasm
Similarity search - Function
Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsRobinson, R.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The crystal structure of the C-terminus of adseverin reveals the actin-binding interface.
Authors: Chumnarnsilpa, S. / Lee, W.L. / Nag, S. / Kannan, B. / Larsson, M. / Burtnick, L.D. / Robinson, R.C.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adseverin
C: Adseverin
G: Adseverin
E: Adseverin
F: Adseverin
H: Adseverin
D: Adseverin
B: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,32931
Polymers335,4078
Non-polymers92223
Water00
1
A: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
G: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0063
Polymers41,9261
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
H: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
B: Adseverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers41,9261
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.644, 90.384, 98.839
Angle α, β, γ (deg.)88.79, 88.26, 76.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H
13A
23B
33C
43D
53E
63F
73G
83H
14A
24C
34G
44E
54F
64H
74D
84B
15A
25C
35G
45E
55F
65H
75D
85B
16A
26C
36G
46E
56F
66H
76D
86B
17A
27C
37G
47E
57F
67H
77D
87B
18A
28C
38G
48E
58F
68H
78D
88B
19A
29C
39G
49E
59F
69H
79D
89B
110A
210C
310G
410E
510F
610H
710D
810B
111A
211C
311G
411E
511F
611H
711D
811B
112A
212C
312G
412E
512F
612H
712D
812B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALILEILEAA398 - 40054 - 56
211VALVALILEILEBH398 - 40054 - 56
311VALVALILEILECB398 - 40054 - 56
411VALVALILEILEDG398 - 40054 - 56
511VALVALILEILEED398 - 40054 - 56
611VALVALILEILEFE398 - 40054 - 56
711VALVALILEILEGC398 - 40054 - 56
811VALVALILEILEHF398 - 40054 - 56
121GLYGLYASNASNAA422 - 44478 - 100
221GLYGLYASNASNBH422 - 44478 - 100
321GLYGLYASNASNCB422 - 44478 - 100
421GLYGLYASNASNDG422 - 44478 - 100
521GLYGLYASNASNED422 - 44478 - 100
621GLYGLYASNASNFE422 - 44478 - 100
721GLYGLYASNASNGC422 - 44478 - 100
821GLYGLYASNASNHF422 - 44478 - 100
131GLNGLNGLNGLNAA467 - 475123 - 131
231GLNGLNGLNGLNBH467 - 475123 - 131
331GLNGLNGLNGLNCB467 - 475123 - 131
431GLNGLNGLNGLNDG467 - 475123 - 131
531GLNGLNGLNGLNED467 - 475123 - 131
631GLNGLNGLNGLNFE467 - 475123 - 131
731GLNGLNGLNGLNGC467 - 475123 - 131
831GLNGLNGLNGLNHF467 - 475123 - 131
112ALAALAGLYGLYAA445 - 466101 - 122
212ALAALAGLYGLYBH445 - 466101 - 122
312ALAALAGLYGLYCB445 - 466101 - 122
412ALAALAGLYGLYDG445 - 466101 - 122
512ALAALAGLYGLYED445 - 466101 - 122
612ALAALAGLYGLYFE445 - 466101 - 122
712ALAALAGLYGLYGC445 - 466101 - 122
812ALAALAGLYGLYHF445 - 466101 - 122
113GLNGLNGLYGLYAA410 - 42166 - 77
213GLNGLNGLYGLYBH410 - 42166 - 77
313GLNGLNGLYGLYCB410 - 42166 - 77
413GLNGLNGLYGLYDG410 - 42166 - 77
513GLNGLNGLYGLYED410 - 42166 - 77
613GLNGLNGLYGLYFE410 - 42166 - 77
713GLNGLNGLYGLYGC410 - 42166 - 77
813GLNGLNGLYGLYHF410 - 42166 - 77
114ARGARGLYSLYSAA615 - 622271 - 278
214ARGARGLYSLYSCB615 - 622271 - 278
314ARGARGLYSLYSGC615 - 622271 - 278
414ARGARGLYSLYSED615 - 622271 - 278
514ARGARGLYSLYSFE615 - 622271 - 278
614ARGARGLYSLYSHF615 - 622271 - 278
714ARGARGLYSLYSDG615 - 622271 - 278
814ARGARGLYSLYSBH615 - 622271 - 278
124ASPASPLYSLYSAA643 - 660299 - 316
224ASPASPLYSLYSCB643 - 660299 - 316
324ASPASPLYSLYSGC643 - 660299 - 316
424ASPASPLYSLYSED643 - 660299 - 316
524ASPASPLYSLYSFE643 - 660299 - 316
624ASPASPLYSLYSHF643 - 660299 - 316
724ASPASPLYSLYSDG643 - 660299 - 316
824ASPASPLYSLYSBH643 - 660299 - 316
134PROPROGLNGLNAA690 - 696346 - 352
234PROPROGLNGLNCB690 - 696346 - 352
334PROPROGLNGLNGC690 - 696346 - 352
434PROPROGLNGLNED690 - 696346 - 352
534PROPROGLNGLNFE690 - 696346 - 352
634PROPROGLNGLNHF690 - 696346 - 352
734PROPROGLNGLNDG690 - 696346 - 352
834PROPROGLNGLNBH690 - 696346 - 352
115THRTHRGLYGLYAA623 - 633279 - 289
215THRTHRGLYGLYCB623 - 633279 - 289
315THRTHRGLYGLYGC623 - 633279 - 289
415THRTHRGLYGLYED623 - 633279 - 289
515THRTHRGLYGLYFE623 - 633279 - 289
615THRTHRGLYGLYHF623 - 633279 - 289
715THRTHRGLYGLYDG623 - 633279 - 289
815THRTHRGLYGLYBH623 - 633279 - 289
116GLUGLUGLUGLUAA634 - 642290 - 298
216GLUGLUGLUGLUCB634 - 642290 - 298
316GLUGLUGLUGLUGC634 - 642290 - 298
416GLUGLUGLUGLUED634 - 642290 - 298
516GLUGLUGLUGLUFE634 - 642290 - 298
616GLUGLUGLUGLUHF634 - 642290 - 298
716GLUGLUGLUGLUDG634 - 642290 - 298
816GLUGLUGLUGLUBH634 - 642290 - 298
117ASPASPLYSLYSAA661 - 667317 - 323
217ASPASPLYSLYSCB661 - 667317 - 323
317ASPASPLYSLYSGC661 - 667317 - 323
417ASPASPLYSLYSED661 - 667317 - 323
517ASPASPLYSLYSFE661 - 667317 - 323
617ASPASPLYSLYSHF661 - 667317 - 323
717ASPASPLYSLYSDG661 - 667317 - 323
817ASPASPLYSLYSBH661 - 667317 - 323
118GLUGLUTRPTRPAA699 - 706355 - 362
218GLUGLUTRPTRPCB699 - 706355 - 362
318GLUGLUTRPTRPGC699 - 706355 - 362
418GLUGLUTRPTRPED699 - 706355 - 362
518GLUGLUTRPTRPFE699 - 706355 - 362
618GLUGLUTRPTRPHF699 - 706355 - 362
718GLUGLUTRPTRPDG699 - 706355 - 362
818GLUGLUTRPTRPBH699 - 706355 - 362
119ASNASNTRPTRPAA536 - 553192 - 209
219ASNASNTRPTRPCB536 - 553192 - 209
319ASNASNTRPTRPGC536 - 553192 - 209
419ASNASNTRPTRPED536 - 553192 - 209
519ASNASNTRPTRPFE536 - 553192 - 209
619ASNASNTRPTRPHF536 - 553192 - 209
719ASNASNTRPTRPDG536 - 553192 - 209
819ASNASNTRPTRPBH536 - 553192 - 209
129LEULEUARGARGAA573 - 579229 - 235
229LEULEUARGARGCB573 - 579229 - 235
329LEULEUARGARGGC573 - 579229 - 235
429LEULEUARGARGED573 - 579229 - 235
529LEULEUARGARGFE573 - 579229 - 235
629LEULEUARGARGHF573 - 579229 - 235
729LEULEUARGARGDG573 - 579229 - 235
829LEULEUARGARGBH573 - 579229 - 235
139PROPROASNASNAA509 - 518165 - 174
239PROPROASNASNCB509 - 518165 - 174
339PROPROASNASNGC509 - 518165 - 174
439PROPROASNASNED509 - 518165 - 174
539PROPROASNASNFE509 - 518165 - 174
639PROPROASNASNHF509 - 518165 - 174
739PROPROASNASNDG509 - 518165 - 174
839PROPROASNASNBH509 - 518165 - 174
1110VALVALVALVALAA554 - 572210 - 228
2110VALVALVALVALCB554 - 572210 - 228
3110VALVALVALVALGC554 - 572210 - 228
4110VALVALVALVALED554 - 572210 - 228
5110VALVALVALVALFE554 - 572210 - 228
6110VALVALVALVALHF554 - 572210 - 228
7110VALVALVALVALDG554 - 572210 - 228
8110VALVALVALVALBH554 - 572210 - 228
1111ILEILELEULEUAA525 - 535181 - 191
2111ILEILELEULEUCB525 - 535181 - 191
3111ILEILELEULEUGC525 - 535181 - 191
4111ILEILELEULEUED525 - 535181 - 191
5111ILEILELEULEUFE525 - 535181 - 191
6111ILEILELEULEUHF525 - 535181 - 191
7111ILEILELEULEUDG525 - 535181 - 191
8111ILEILELEULEUBH525 - 535181 - 191
1112ILEILELYSLYSAA580 - 596236 - 252
2112ILEILELYSLYSCB580 - 596236 - 252
3112ILEILELYSLYSGC580 - 596236 - 252
4112ILEILELYSLYSED580 - 596236 - 252
5112ILEILELYSLYSFE580 - 596236 - 252
6112ILEILELYSLYSHF580 - 596236 - 252
7112ILEILELYSLYSDG580 - 596236 - 252
8112ILEILELYSLYSBH580 - 596236 - 252

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
Adseverin / Scinderin


Mass: 41925.914 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCIN, KIAA1905 / Plasmid: pSY5 (modified pET21d) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus (DE3)-RIL / References: UniProt: Q9Y6U3
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.749113 Å3/Da / Density % sol: 29.678656 % / Mosaicity: 0.829 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4000, 200mM sodium isothiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 16.78 / Number: 79198 / Rmerge(I) obs: 0.04 / Χ2: 0.91 / D res high: 3 Å / D res low: 30 Å / Num. obs: 41218 / % possible obs: 90.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.443088.310.0260.6811.9
5.126.4490.410.0310.8741.9
4.485.1289.210.0280.7711.9
4.074.4889.510.0310.8181.9
3.784.0790.410.0390.9262
3.563.7892.310.0511.011.9
3.383.5693.510.0660.9761.9
3.233.3893.610.0870.9161.9
3.113.2391.110.1050.9591.9
33.118510.1421.1821.8
ReflectionResolution: 3→30 Å / Num. obs: 41218 / % possible obs: 90.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Χ2: 0.908 / Net I/σ(I): 16.784
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.142 / Num. unique all: 3909 / Χ2: 1.182 / % possible all: 85

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å29.92 Å
Translation2.99 Å29.92 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P8X
Resolution: 3→29.92 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.842 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.783 / SU B: 61.231 / SU ML: 0.517 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.651 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2084 5.1 %RANDOM
Rwork0.244 39127 --
obs0.247 41211 90.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.73 Å2 / Biso mean: 38.605 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.05 Å20.08 Å2
2---0.05 Å2-0.04 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19089 0 23 0 19112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02219516
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.95126432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35452350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44224.865962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.974153389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.15115109
X-RAY DIFFRACTIONr_chiral_restr0.0670.22845
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214855
X-RAY DIFFRACTIONr_nbd_refined0.2030.28005
X-RAY DIFFRACTIONr_nbtor_refined0.310.212808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2638
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.2326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.228
X-RAY DIFFRACTIONr_mcbond_it0.1681.512037
X-RAY DIFFRACTIONr_mcangle_it0.298218999
X-RAY DIFFRACTIONr_scbond_it0.30638623
X-RAY DIFFRACTIONr_scangle_it0.4954.57433
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A252TIGHT POSITIONAL0.020.05
1B252TIGHT POSITIONAL0.020.05
1C252TIGHT POSITIONAL0.020.05
1D252TIGHT POSITIONAL0.030.05
1E252TIGHT POSITIONAL0.030.05
1F252TIGHT POSITIONAL0.020.05
1G252TIGHT POSITIONAL0.020.05
1H252TIGHT POSITIONAL0.020.05
1A252TIGHT THERMAL0.030.5
1B252TIGHT THERMAL0.030.5
1C252TIGHT THERMAL0.030.5
1D252TIGHT THERMAL0.040.5
1E252TIGHT THERMAL0.030.5
1F252TIGHT THERMAL0.030.5
1G252TIGHT THERMAL0.030.5
1H252TIGHT THERMAL0.040.5
2A164TIGHT POSITIONAL0.020.05
2B164TIGHT POSITIONAL0.020.05
2C164TIGHT POSITIONAL0.020.05
2D164TIGHT POSITIONAL0.020.05
2E164TIGHT POSITIONAL0.020.05
2F164TIGHT POSITIONAL0.020.05
2G164TIGHT POSITIONAL0.020.05
2H164TIGHT POSITIONAL0.020.05
2A164TIGHT THERMAL0.030.5
2B164TIGHT THERMAL0.020.5
2C164TIGHT THERMAL0.030.5
2D164TIGHT THERMAL0.030.5
2E164TIGHT THERMAL0.020.5
2F164TIGHT THERMAL0.020.5
2G164TIGHT THERMAL0.030.5
2H164TIGHT THERMAL0.030.5
3A99TIGHT POSITIONAL0.020.05
3B99TIGHT POSITIONAL0.020.05
3C99TIGHT POSITIONAL0.020.05
3D99TIGHT POSITIONAL0.020.05
3E99TIGHT POSITIONAL0.020.05
3F99TIGHT POSITIONAL0.020.05
3G99TIGHT POSITIONAL0.020.05
3H99TIGHT POSITIONAL0.020.05
3A99TIGHT THERMAL0.030.5
3B99TIGHT THERMAL0.020.5
3C99TIGHT THERMAL0.030.5
3D99TIGHT THERMAL0.030.5
3E99TIGHT THERMAL0.030.5
3F99TIGHT THERMAL0.030.5
3G99TIGHT THERMAL0.030.5
3H99TIGHT THERMAL0.030.5
4A274TIGHT POSITIONAL0.020.05
4C274TIGHT POSITIONAL0.020.05
4G274TIGHT POSITIONAL0.020.05
4E274TIGHT POSITIONAL0.020.05
4F274TIGHT POSITIONAL0.020.05
4H274TIGHT POSITIONAL0.020.05
4D274TIGHT POSITIONAL0.020.05
4B274TIGHT POSITIONAL0.020.05
4A274TIGHT THERMAL0.030.5
4C274TIGHT THERMAL0.030.5
4G274TIGHT THERMAL0.020.5
4E274TIGHT THERMAL0.020.5
4F274TIGHT THERMAL0.030.5
4H274TIGHT THERMAL0.040.5
4D274TIGHT THERMAL0.030.5
4B274TIGHT THERMAL0.030.5
5A85TIGHT POSITIONAL0.020.05
5C85TIGHT POSITIONAL0.020.05
5G85TIGHT POSITIONAL0.010.05
5E85TIGHT POSITIONAL0.020.05
5F85TIGHT POSITIONAL0.010.05
5H85TIGHT POSITIONAL0.020.05
5D85TIGHT POSITIONAL0.020.05
5B85TIGHT POSITIONAL0.020.05
5A85TIGHT THERMAL0.030.5
5C85TIGHT THERMAL0.020.5
5G85TIGHT THERMAL0.030.5
5E85TIGHT THERMAL0.020.5
5F85TIGHT THERMAL0.020.5
5H85TIGHT THERMAL0.030.5
5D85TIGHT THERMAL0.020.5
5B85TIGHT THERMAL0.020.5
6A74TIGHT POSITIONAL0.020.05
6C74TIGHT POSITIONAL0.010.05
6G74TIGHT POSITIONAL0.020.05
6E74TIGHT POSITIONAL0.020.05
6F74TIGHT POSITIONAL0.020.05
6H74TIGHT POSITIONAL0.020.05
6D74TIGHT POSITIONAL0.020.05
6B74TIGHT POSITIONAL0.020.05
6A74TIGHT THERMAL0.020.5
6C74TIGHT THERMAL0.020.5
6G74TIGHT THERMAL0.020.5
6E74TIGHT THERMAL0.020.5
6F74TIGHT THERMAL0.030.5
6H74TIGHT THERMAL0.020.5
6D74TIGHT THERMAL0.020.5
6B74TIGHT THERMAL0.020.5
7A55TIGHT POSITIONAL0.010.05
7C55TIGHT POSITIONAL0.020.05
7G55TIGHT POSITIONAL0.020.05
7E55TIGHT POSITIONAL0.010.05
7F55TIGHT POSITIONAL0.020.05
7H55TIGHT POSITIONAL0.020.05
7D55TIGHT POSITIONAL0.030.05
7B55TIGHT POSITIONAL0.020.05
7A55TIGHT THERMAL0.030.5
7C55TIGHT THERMAL0.030.5
7G55TIGHT THERMAL0.020.5
7E55TIGHT THERMAL0.030.5
7F55TIGHT THERMAL0.030.5
7H55TIGHT THERMAL0.040.5
7D55TIGHT THERMAL0.030.5
7B55TIGHT THERMAL0.030.5
8A66TIGHT POSITIONAL0.010.05
8C66TIGHT POSITIONAL0.020.05
8G66TIGHT POSITIONAL0.020.05
8E66TIGHT POSITIONAL0.020.05
8F66TIGHT POSITIONAL0.010.05
8H66TIGHT POSITIONAL0.020.05
8D66TIGHT POSITIONAL0.020.05
8B66TIGHT POSITIONAL0.020.05
8A66TIGHT THERMAL0.020.5
8C66TIGHT THERMAL0.040.5
8G66TIGHT THERMAL0.030.5
8E66TIGHT THERMAL0.030.5
8F66TIGHT THERMAL0.020.5
8H66TIGHT THERMAL0.030.5
8D66TIGHT THERMAL0.020.5
8B66TIGHT THERMAL0.030.5
9A296TIGHT POSITIONAL0.020.05
9C296TIGHT POSITIONAL0.020.05
9G296TIGHT POSITIONAL0.010.05
9E296TIGHT POSITIONAL0.020.05
9F296TIGHT POSITIONAL0.020.05
9H296TIGHT POSITIONAL0.020.05
9D296TIGHT POSITIONAL0.020.05
9B296TIGHT POSITIONAL0.020.05
9A296TIGHT THERMAL0.040.5
9C296TIGHT THERMAL0.030.5
9G296TIGHT THERMAL0.030.5
9E296TIGHT THERMAL0.030.5
9F296TIGHT THERMAL0.030.5
9H296TIGHT THERMAL0.040.5
9D296TIGHT THERMAL0.030.5
9B296TIGHT THERMAL0.030.5
10A135TIGHT POSITIONAL0.020.05
10C135TIGHT POSITIONAL0.020.05
10G135TIGHT POSITIONAL0.020.05
10E135TIGHT POSITIONAL0.020.05
10F135TIGHT POSITIONAL0.020.05
10H135TIGHT POSITIONAL0.020.05
10D135TIGHT POSITIONAL0.020.05
10B135TIGHT POSITIONAL0.020.05
10A135TIGHT THERMAL0.040.5
10C135TIGHT THERMAL0.040.5
10G135TIGHT THERMAL0.030.5
10E135TIGHT THERMAL0.040.5
10F135TIGHT THERMAL0.030.5
10H135TIGHT THERMAL0.040.5
10D135TIGHT THERMAL0.030.5
10B135TIGHT THERMAL0.030.5
11A81TIGHT POSITIONAL0.020.05
11C81TIGHT POSITIONAL0.020.05
11G81TIGHT POSITIONAL0.010.05
11E81TIGHT POSITIONAL0.030.05
11F81TIGHT POSITIONAL0.020.05
11H81TIGHT POSITIONAL0.020.05
11D81TIGHT POSITIONAL0.020.05
11B81TIGHT POSITIONAL0.020.05
11A81TIGHT THERMAL0.040.5
11C81TIGHT THERMAL0.040.5
11G81TIGHT THERMAL0.030.5
11E81TIGHT THERMAL0.040.5
11F81TIGHT THERMAL0.030.5
11H81TIGHT THERMAL0.050.5
11D81TIGHT THERMAL0.030.5
11B81TIGHT THERMAL0.030.5
12A137TIGHT POSITIONAL0.020.05
12C137TIGHT POSITIONAL0.020.05
12G137TIGHT POSITIONAL0.010.05
12E137TIGHT POSITIONAL0.020.05
12F137TIGHT POSITIONAL0.020.05
12H137TIGHT POSITIONAL0.020.05
12D137TIGHT POSITIONAL0.010.05
12B137TIGHT POSITIONAL0.020.05
12A137TIGHT THERMAL0.030.5
12C137TIGHT THERMAL0.030.5
12G137TIGHT THERMAL0.020.5
12E137TIGHT THERMAL0.040.5
12F137TIGHT THERMAL0.020.5
12H137TIGHT THERMAL0.030.5
12D137TIGHT THERMAL0.020.5
12B137TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.995→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 133 -
Rwork0.349 2647 -
all-2780 -
obs--83.01 %
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)
14.2721-1.0834-0.34645.2599-0.752717.02840.22260.13440.3326-0.2123-0.21770.4536-0.0201-0.2219-0.005-0.3687-0.0036-0.0552-0.3246-0.1517-0.217429.5813-45.8517-30.562
23.3569-2.16550.040610.87560.780411.03510.35240.46210.1546-0.6442-0.3797-0.22320.1102-0.00710.0273-0.5338-0.03560.0246-0.23840.0415-0.318832.7849-49.23-57.6537
34.5406-5.36923.728118.6282-7.178510.36740.79730.4503-0.198-1.2064-0.90370.13451.91130.78770.10640.13640.27950.2422-0.08360.1119-0.142638.4473-70.8589-44.6171
43.5297-3.5093-1.405615.62661.16684.2942-0.2041-0.63880.01710.43010.1828-0.1294-0.3351-0.02070.0212-0.17960.0111-0.0258-0.2089-0.0726-0.317832.64128.4602-78.7288
55.8878-0.863-0.35887.81912.360913.60580.28970.3639-0.2944-0.198-0.207-0.13270.56630.229-0.0827-0.33420.0621-0.0875-0.34410.0449-0.280841.5965-17.3239-82.7858
61.9474-3.39611.69416.4282-0.864816.1556-0.0996-0.12650.14120.22980.1617-0.2698-0.23950.4494-0.0621-0.1039-0.174-0.0487-0.3037-0.0349-0.232539.0903-4.1077-104.7253
711.1388-5.591-1.435313.96152.60122.2788-0.04160.68290.1891-0.3630.3377-0.021-0.3503-0.4213-0.2961-0.2711-0.17250.0538-0.23390.0953-0.315818.3169-24.2384-3.3747
85.8586-1.40290.18347.1161-1.259511.2504-0.3194-0.0073-0.28220.5040.1147-0.31550.58970.18430.2047-0.2802-0.0277-0.0469-0.4496-0.1004-0.341335.4475-45.8089-0.0097
96.3209-2.0555-2.77199.15452.332211.131-0.09710.10180.1242-0.46450.10230.64810.1077-0.3328-0.0052-0.3363-0.1036-0.1236-0.1641-0.0587-0.285623.4807-39.895423.0362
105.96230.16221.68033.42211.094913.73020.12970.0284-0.3315-0.0386-0.0750.00710.46870.3273-0.0547-0.4926-0.01420.0536-0.3809-0.0155-0.309819.873932.3391-54.6523
117.3589-3.57690.6911.1111-0.93896.21570.59830.5901-0.3198-1.3207-0.37430.5762-0.11610.0849-0.2240.03630.3392-0.0792-0.1695-0.1201-0.418513.681933.1214-81.5265
123.83-4.143-0.7959.5365.78729.51150.0884-0.238-0.1361-0.2784-0.0429-0.33620.38561.1239-0.0454-0.16690.1219-0.0109-0.150.0318-0.24869.760556.1738-69.7381
1311.1162-9.8027-2.027715.6254-0.6623.2496-0.00570.66260.1417-0.07460.06380.0652-0.251-0.1512-0.0581-0.1374-0.05530.0511-0.2179-0.0073-0.328931.696811.6294-28.2461
147.0944-3.3136-1.840712.14180.666911.9739-0.1423-0.30730.36270.84080.158-0.123-0.097-0.3925-0.0157-0.3523-0.0064-0.0063-0.39540.0426-0.286116.739234.1317-23.9714
156.1453-4.16955.88196.0081-6.041715.232-0.1939-0.07220.20340.1866-0.0024-0.2133-1.562-0.10420.19630.25790.08420.1003-0.1361-0.0254-0.36627.680325.076-1.9468
164.98091.59431.61611.27383.436226.91170.09530.2897-0.096-0.4438-0.11530.0191-0.0510.43520.02-0.06970.07410.0831-0.22960.0408-0.08965.7372-0.715-26.424
1710.5603-2.55631.181712.78582.41059.6804-0.5397-0.88760.39170.81770.35530.2106-0.6718-0.62430.1844-0.09730.13660.1128-0.25070.1631-0.36237.04154.98010.222
186.9183-5.26811.467613.3866-2.33095.4932-0.2221-0.3066-0.62590.60180.14930.60320.781-0.36450.0728-0.1257-0.1099-0.0571-0.2856-0.0232-0.1855-8.471921.6894-11.7732
197.2374-2.1302-0.254613.198-2.62796.02280.0374-0.1835-0.18830.40920.2630.297-0.0208-0.2499-0.3004-0.386-0.0052-0.0249-0.2567-0.023-0.307316.0057-23.0567-53.7569
207.23640.2063-0.38226.2678-3.300115.78020.4444-0.22910.89050.20320.01010.1521-2.1958-0.4745-0.45460.4580.39440.5073-0.2762-0.0665-0.07278.51473.3354-57.4518
211.2315-2.6646-0.24577.5513.506813.9888-0.1851-0.2223-0.3490.50780.30.0609-0.2137-0.8982-0.1149-0.03610.04910.2882-0.11460.2235-0.1677.4889-10.5965-79.1561
224.7001-1.5504-1.25412.633-2.000714.10310.0081-0.01870.3877-0.3306-0.3279-0.0968-0.5957-0.19080.3198-0.4069-0.0839-0.0383-0.4037-0.0409-0.155744.612-12.43-52.1215
234.6397-2.56662.34038.9626-0.56119.6218-0.3872-0.39560.17180.58190.4706-0.13050.019-0.013-0.0833-0.3717-0.0952-0.0052-0.3996-0.0916-0.363542.1426-17.8311-24.9741
243.7541-3.6863-1.90818.11863.28149.3589-0.39220.12920.27180.16120.3255-0.4823-0.81540.28530.0667-0.3073-0.0804-0.0023-0.4085-0.0184-0.191159.062-34.2836-36.5193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A396 - 494
2X-RAY DIFFRACTION2A509 - 609
3X-RAY DIFFRACTION3A610 - 715
4X-RAY DIFFRACTION4B396 - 494
5X-RAY DIFFRACTION5B509 - 609
6X-RAY DIFFRACTION6B610 - 715
7X-RAY DIFFRACTION7C396 - 494
8X-RAY DIFFRACTION8C509 - 609
9X-RAY DIFFRACTION9C610 - 712
10X-RAY DIFFRACTION10D396 - 494
11X-RAY DIFFRACTION11D509 - 609
12X-RAY DIFFRACTION12D610 - 712
13X-RAY DIFFRACTION13E396 - 494
14X-RAY DIFFRACTION14E509 - 603
15X-RAY DIFFRACTION15E613 - 715
16X-RAY DIFFRACTION16F396 - 494
17X-RAY DIFFRACTION17F509 - 609
18X-RAY DIFFRACTION18F610 - 715
19X-RAY DIFFRACTION19G396 - 494
20X-RAY DIFFRACTION20G509 - 609
21X-RAY DIFFRACTION21G610 - 715
22X-RAY DIFFRACTION22H396 - 494
23X-RAY DIFFRACTION23H509 - 609
24X-RAY DIFFRACTION24H610 - 715

+
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