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- PDB-1h8t: Echovirus 11 -

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Basic information

Entry
Database: PDB / ID: 1h8t
TitleEchovirus 11
Components(ECHOVIRUS 11 COAT PROTEIN ...) x 4
KeywordsVIRUS / ECHOVIRUS COAT PROTEIN / ECHOVIRUS / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
12-AMINO-DODECANOIC ACID / MYRISTIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesECHOVIRUS 11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsStuart, A. / McKee, T. / Williams, P.A. / Harley, C. / Stuart, D.I. / Brown, T.D.K. / Lea, S.M.
CitationJournal: J.Virol. / Year: 2002
Title: Determination of the Structure of a Decay Accelerating Factor-Binding Clinical Isolate of Echovirus 11 Allows Mapping of Mutants with Altered Receptor Requirements for Infection
Authors: Stuart, A. / Mckee, T. / Williams, P.A. / Harley, C. / Shen, S. / Stuart, D.I. / Brown, T.D.K. / Lea, S.M.
History
DepositionFeb 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2002Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5546
Polymers95,1114
Non-polymers4442
Water19811
1
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,733,265360
Polymers5,706,643240
Non-polymers26,622120
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 478 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)477,77230
Polymers475,55420
Non-polymers2,21910
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 573 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)573,32636
Polymers570,66424
Non-polymers2,66212
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.91 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,911,088120
Polymers1,902,21480
Non-polymers8,87440
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)300.850, 300.850, 1476.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.507091, -0.649919, 0.566095), (0.861614, 0.36558, -0.352096), (0.02188, 0.666301, 0.745362)-208.96134, 129.96817, 93.99385
3generate(-0.290451, -0.189976, 0.937842), (0.744203, -0.660932, 0.096598), (0.601498, 0.726001, 0.333349)-346.18311, -35.65695, 246.07907
4generate(-0.290451, 0.744203, 0.601498), (-0.189976, -0.660932, 0.726001), (0.937842, 0.096598, 0.333349)-222.02949, -267.98708, 246.07905
5generate(0.507091, 0.861614, 0.02188), (-0.649919, 0.36558, 0.666301), (0.566095, -0.352096, 0.745362)-8.07656, -245.94988, 93.99383
6generate(-0.816394, -0.114204, 0.56609), (-0.114204, -0.928965, -0.352111), (0.56609, -0.352111, 0.745359)-208.95555, 129.97974, 93.99491
7generate(-0.5, 0.866025, -5.0E-6), (-0.866025, -0.5, -1.6E-5), (-1.6E-5, -4.0E-6, 1)0.00545, 0.01179
8generate(0.492634, 0.641558, -0.587975), (-0.869962, 0.380045, -0.314217), (0.021869, 0.66631, 0.745354)217.04142, 115.99204, 93.99669
9generate(0.789721, -0.477399, -0.385266), (-0.120573, 0.494979, -0.860499), (0.6015, 0.726007, 0.333334)142.21604, 317.63974, 246.08475
10generate(-0.019303, -0.944486, 0.327985), (0.346511, -0.314034, -0.883919), (0.937847, 0.096588, 0.333337)-121.06457, 326.28462, 246.08365
11generate(-0.442118, 0.896957, 1.0E-5), (0.896957, 0.442118, 1.6E-5), (1.0E-5, 1.6E-5, -1)-0.00012, -0.00794, 738.26552
12generate(0.548637, 0.615257, -0.566088), (0.835775, -0.421309, 0.352107), (-0.021862, -0.666301, -0.745362)208.96219, -129.97455, 644.27167
13generate(0.795938, -0.508829, -0.327989), (0.068512, -0.462599, 0.883917), (-0.601489, -0.726014, -0.333339)121.07326, -326.28002, 492.18252
14generate(-0.041977, -0.921852, 0.385262), (-0.3445, 0.37531, 0.860501), (-0.937848, -0.096601, -0.333332)-142.2074, -317.63686, 492.18011
15generate(-0.807138, -0.053029, 0.587977), (0.167507, 0.934455, 0.314221), (-0.566101, 0.35211, -0.745351)-217.03487, -115.98963, 644.26777
16generate(0.258512, -0.782753, -0.566099), (-0.782753, -0.513153, 0.352095), (-0.566099, 0.352095, -0.745359)208.97001, -129.96423, 644.27061
17generate(-0.555729, -0.831364, -2.0E-6), (-0.831364, 0.555729, 5.0E-6), (-2.0E-6, 5.0E-6, -1)0.00804, 0.00216, 738.26552
18generate(-0.99812, 0.057246, -0.021878), (0.057246, 0.743485, -0.666297), (-0.021878, -0.666297, -0.745365)8.08277, 245.9525, 644.27276
19generate(-0.457293, 0.655048, -0.601494), (0.655048, -0.209356, -0.726004), (-0.601494, -0.726004, -0.333351)222.0352, 267.99178, 492.18713
20generate(0.319349, 0.1359, -0.937842), (0.1359, -0.986002, -0.096603), (-0.937842, -0.096603, -0.333348)346.19034, 35.66246, 492.1858
21generate(0.81933, -0.152792, 0.552588), (0.424571, -0.486004, -0.763898), (0.385277, 0.860497, -0.333326)-203.97739, 281.98107, 492.17138
22generate(0.295918, -0.220166, 0.929494), (-0.220166, -0.962596, -0.157913), (0.929494, -0.157913, -0.333323)-343.10381, 58.29547, 492.17002
23generate(-0.019303, 0.346511, 0.937847), (-0.944486, -0.314034, 0.096588), (0.327985, -0.883919, 0.333337)-346.18709, -35.64811, 246.0877
24generate(0.309291, 0.764111, 0.566103), (-0.747404, 0.563391, -0.352105), (-0.587985, -0.314204, 0.745351)-208.96624, 129.97718, 94.00182
25generate(0.827595, 0.455525, 0.328), (0.09872, 0.457108, -0.883915), (-0.552577, 0.763904, 0.333331)-121.07581, 326.2828, 246.0899
26generate(-0.338633, -0.146205, 0.92949), (-0.723549, 0.671969, -0.157906), (-0.601502, -0.726004, -0.333337)-343.10025, 58.29149, 492.18186
27generate(-0.277352, 0.785954, 0.552587), (0.208618, 0.610694, -0.763892), (-0.937845, -0.096588, -0.333342)-203.97472, 281.97765, 492.18363
28generate(0.548637, 0.835775, -0.021862), (0.615257, -0.421309, -0.666301), (-0.566088, 0.352107, -0.745362)8.06993, 245.95412, 644.2717
29generate(0.997846, -0.065593, 1.3E-5), (-0.065593, -0.997846), (1.3E-5, -1)-0.00479, 0.00418, 738.26552
30generate(0.449484, -0.67249, 0.587981), (-0.893021, -0.322163, 0.314205), (-0.021874, -0.666309, -0.745354)-217.03989, -115.9777, 644.26883
31generate(-0.499282, 0.66736, -0.552582), (-0.623642, 0.165939, 0.763895), (0.601488, 0.726013, 0.333343)203.98037, -281.97468, 246.08124
32generate(0.309735, 0.200281, -0.92949), (-0.156554, 0.974964, 0.157911), (0.937846, 0.096605, 0.333335)343.10736, -58.28942, 246.08432
33generate(0.309291, -0.747404, -0.587985), (0.764111, 0.563391, -0.314204), (0.566103, -0.352105, 0.745351)217.04855, 115.98124, 93.99776
34generate(-0.5, -0.866025, -1.6E-5), (0.866025, -0.5, -4.0E-6), (-5.0E-6, -1.6E-5, 1)0.01293, 0.00117
35generate(-0.999726, 0.008347, 0.021864), (0.008347, -0.745639, 0.666298), (0.021864, 0.666298, 0.745365)-8.06364, -245.94911, 93.99276
36generate(0.018585, -0.368364, -0.929496), (0.92262, -0.351905, 0.157909), (-0.385262, -0.860506, 0.33332)343.1116, -58.2903, 246.09657
37generate(-0.328301, -0.766069, -0.552591), (0.168101, -0.623062, 0.763895), (-0.929495, 0.157896, 0.333329)203.98552, -281.97612, 246.09307
38generate(-0.838626, -0.434883, -0.328), (-0.434883, 0.171952, 0.883917), (-0.328, 0.883917, -0.333326)121.08295, -326.27967, 492.17389
39generate(-0.807138, 0.167507, -0.566101), (-0.053029, 0.934455, 0.35211), (0.587977, 0.314221, -0.745351)208.97243, -129.97496, 644.2637
40generate(-0.277352, 0.208618, -0.937845), (0.785954, 0.610694, -0.096588), (0.552587, -0.763892, -0.333342)346.19368, 35.65158, 492.17955
41generate(0.81933, 0.424571, 0.385277), (-0.152792, -0.486004, 0.860497), (0.552588, -0.763898, -0.333326)-142.2185, -317.63432, 492.17386
42generate(0.789721, -0.120573, 0.6015), (-0.477399, 0.494979, 0.726007), (-0.385266, -0.860499, 0.333334)-222.03238, -267.99032, 246.09129
43generate(0.309735, -0.156554, 0.937846), (0.200281, 0.974964, 0.096605), (-0.92949, 0.157911, 0.333335)-346.18694, -35.66069, 246.0909
44generate(0.042695, 0.366352, 0.929496), (0.943718, 0.290629, -0.157897), (-0.327985, 0.883924, -0.333324)-343.1048, 58.28292, 492.17322
45generate(0.357642, 0.725507, 0.58799), (0.725507, -0.612298, 0.314214), (0.58799, 0.314214, -0.745344)-217.04537, -115.98637, 644.26086
46generate(-0.499282, -0.623642, 0.601488), (0.66736, 0.165939, 0.726013), (-0.552582, 0.763895, 0.333343)-222.0223, -267.99591, 246.0853
47generate(-0.77736, 0.497273, 0.385266), (0.497273, 0.110677, 0.860506), (0.385266, 0.860506, -0.333317)-142.20903, -317.64088, 492.16787
48generate(0.042695, 0.943718, -0.327985), (0.366352, 0.290629, 0.883924), (0.929496, -0.157897, -0.333324)121.0716, -326.2851, 492.17069
49generate(0.827595, 0.09872, -0.552577), (0.455525, 0.457108, 0.763904), (0.328, -0.883915, 0.333331)203.9747, -281.98255, 246.08987
50generate(0.492634, -0.869962, 0.021869), (0.641558, 0.380045, 0.66631), (-0.587975, -0.314217, 0.745354)-8.06899, -245.95785, 94.00073
51generate(0.018585, 0.92262, -0.385262), (-0.368364, -0.351905, -0.860506), (-0.929496, 0.157909, 0.33332)142.21471, 317.64492, 246.09659
52generate(0.795938, 0.068512, -0.601489), (-0.508829, -0.462599, -0.726014), (-0.327989, 0.883917, -0.333339)222.03005, 268.00001, 492.1785
53generate(0.449484, -0.893021, -0.021874), (-0.67249, -0.322163, -0.666309), (0.587981, 0.314205, -0.745354)8.07801, 245.96158, 644.26479
54generate(-0.541989, -0.633173, 0.552575), (-0.633173, -0.124675, -0.763903), (0.552575, -0.763903, -0.333336)-203.96697, 281.98599, 492.17738
55generate(-0.808299, 0.488954, 0.327989), (-0.445213, -0.143057, -0.883923), (-0.385277, -0.860499, 0.333321)-121.06593, 326.28873, 246.0959
56generate(-0.338633, -0.723549, -0.601502), (-0.146205, 0.671969, -0.726004), (0.92949, -0.157906, -0.333337)222.04043, 267.99288, 492.17529
57generate(-0.808299, -0.445213, -0.385277), (0.488954, -0.143057, -0.860499), (0.327989, -0.883923, 0.333321)142.22569, 317.63876, 246.09338
58generate(-0.801913, 0.105857, -0.587987), (0.105857, -0.94343, -0.314219), (-0.587987, -0.314219, 0.745344)217.05167, 115.99178, 94.00466
59generate(-0.328301, 0.168101, -0.929495), (-0.766069, -0.623062, 0.157896), (-0.552591, 0.763895, 0.333329)343.11141, -58.27879, 246.09057
60generate(-0.041977, -0.3445, -0.937848), (-0.921852, 0.37531, -0.096601), (0.385262, 0.860501, -0.333332)346.19463, 35.66306, 492.17356

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Components

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ECHOVIRUS 11 COAT PROTEIN ... , 4 types, 4 molecules ABCD

#1: Protein ECHOVIRUS 11 COAT PROTEIN VP1


Mass: 32786.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ECHOVIRUS 11 / Strain: 207 / References: UniProt: P29813, UniProt: Q8JKE8*PLUS
#2: Protein ECHOVIRUS 11 COAT PROTEIN VP2


Mass: 29048.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ECHOVIRUS 11 / Strain: 207 / References: UniProt: P29813, UniProt: Q8JKE8*PLUS
#3: Protein ECHOVIRUS 11 COAT PROTEIN VP3


Mass: 25897.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ECHOVIRUS 11 / Strain: 207 / References: UniProt: P29813, UniProt: Q8JKE8*PLUS
#4: Protein ECHOVIRUS 11 COAT PROTEIN VP4


Mass: 7378.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ECHOVIRUS 11 / Strain: 207 / References: UniProt: P29813, UniProt: Q8JKE8*PLUS

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Non-polymers , 3 types, 13 molecules

#5: Chemical ChemComp-DOA / 12-AMINO-DODECANOIC ACID


Type: L-peptide linking / Mass: 215.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H25NO2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DBREF IS TO STRAIN GREGORY, NOT SEQUENCE DETAILS ARE AVAILABLE FOR STRAIN 207

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 75

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Sample preparation

CrystalDescription: DATA WERE COLLECTED AT TWO SYNCHROTRONS FOR FINAL NATIVE SET AS ABOVE AND ALSO SRS STAION 7.2
Crystal growpH: 7.5 / Details: 2.0M AMMONIUM SULPHATE, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-Cl1droppH7.4
22.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 411040 / % possible obs: 70 % / Redundancy: 4 % / Rmerge(I) obs: 0.22
Reflection shellResolution: 2.9→3.2 Å / Rmerge(I) obs: 0.35 / % possible all: 35
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 70 % / Num. measured all: 1648270

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D4M
Resolution: 2.9→100 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED WITH STRICT NCS DISORDERED REGIONS ARE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 2029 0.4 %RANDOM
Rwork0.2462 ---
obs0.2462 402349 71.3 %-
Solvent computationBsol: 30.5282 Å2 / ksol: 0.331789 e/Å3
Displacement parametersBiso mean: 17.143 Å2
Baniso -1Baniso -2Baniso -3
1-1.178 Å2-1.509 Å20 Å2
2--1.178 Å20 Å2
3----2.357 Å2
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 30 11 6575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.16534
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.8581.5
X-RAY DIFFRACTIONc_mcangle_it6.4472
X-RAY DIFFRACTIONc_scbond_it5.6672
X-RAY DIFFRACTIONc_scangle_it8.1532.5
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.3883 156
Rwork0.342 34536
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3MYR.PAR
X-RAY DIFFRACTION4PLM-MOD.PAR
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 500 Å / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2

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