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- PDB-2b2d: RNA stemloop operator from bacteriophage QBETA complexed with an ... -

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Basic information

Entry
Database: PDB / ID: 2b2d
TitleRNA stemloop operator from bacteriophage QBETA complexed with an N87S,E89K mutant MS2 capsid
Components
  • 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
  • Coat protein
KeywordsVIRUS/VIRAL PROTEIN/RNA / capsid / complex (capsid protein - RNA hairpin) hairpin / levivirus / VIRUS/VIRAL / protein/RNA / VIRUS-VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHorn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
CitationJournal: Structure / Year: 2006
Title: Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2
Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Advisory
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)53,9185
Polymers53,9185
Non-polymers00
Water2,144119
1
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,235,094300
Polymers3,235,094300
Non-polymers00
Water4,324240
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
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 270 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)269,59125
Polymers269,59125
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 324 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)323,50930
Polymers323,50930
Non-polymers00
Water43224
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
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 10


  • crystal asymmetric unit, crystal frame
  • 539 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)539,18250
Polymers539,18250
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.80, 287.80, 652.60
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.8660254), (0.64549722, 0.372678, 0.66666667), (-0.57735027, -0.33333333, 0.74535599)
3generate(-0.30901699, -0.75576131, -0.57735027), (0.17841104, -0.64235033, 0.74535599), (-0.93417236, 0.127322, 0.33333333)
4generate(-0.30901699, 0.17841104, -0.93417236), (-0.75576131, -0.64235033, 0.127322), (-0.57735027, 0.74535599, 0.33333333)
5generate(0.5, 0.64549722, -0.57735027), (-0.8660254, 0.372678, -0.33333333), (0.66666667, 0.74535599)
6generate(0.30901699, -0.75576131, -0.57735027), (-0.75576131, -0.563661, 0.33333333), (-0.57735027, 0.33333333, -0.74535599)
7generate(-0.35682209, -0.93417236), (-0.93417236, 0.33333333, -0.127322), (0.35682209, 0.872678, -0.33333333)
8generate(0.30901699, 0.17841104, -0.93417236), (-0.17841104, 0.97568366, 0.127322), (0.93417236, 0.127322, 0.33333333)
9generate(0.80901699, 0.11026409, -0.57735027), (0.46708618, 0.47568366, 0.74535599), (0.35682209, -0.872678, 0.33333333)
10generate(0.80901699, -0.46708618, -0.35682209), (0.11026409, -0.47568366, 0.872678), (-0.57735027, -0.74535599, -0.33333333)
DetailsSYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 -Y,X-Y,Z 3555 Y-X,-X,Z 4555 Y,X,-Z 5555 X-Y,-Y,-Z 6555 -X,Y-X,-Z 7555 2/3+X,1/3+Y,1/3+Z 8555 2/3-Y,1/3+X-Y,1/3+Z 9555 2/3+Y-X,1/3-X,1/3+Z 10555 2/3+Y,1/3+X,1/3-Z 11555 2/3+X-Y,1/3-Y,1/3-Z 12555 2/3-X,1/3+Y-X,1/3-Z 13555 1/3+X,2/3+Y,2/3+Z 14555 1/3-Y,2/3+X-Y,2/3+Z 15555 1/3+Y-X,2/3-X,2/3+Z 16555 1/3+Y,2/3+X,2/3-Z 17555 1/3+X-Y,2/3-Y,2/3-Z 18555 1/3-X,2/3+Y-X,2/3-Z WHERE NNN -> OPERATOR NUMBER MMM -> TRANSLATION VECTOR CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY RELATED MOLECULES. SMTRY1 1 1.000000 0.000000 0.000000 0.00000 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 SMTRY1 7 1.000000 0.000000 0.000000 55.34800 SMTRY2 7 0.000000 1.000000 0.000000 31.95518 SMTRY3 7 0.000000 0.000000 1.000000 39.09767 SMTRY1 8 -0.500000 -0.866025 0.000000 55.34800 SMTRY2 8 0.866025 -0.500000 0.000000 31.95518 SMTRY3 8 0.000000 0.000000 1.000000 39.09767 SMTRY1 9 -0.500000 0.866025 0.000000 55.34800 SMTRY2 9 -0.866025 -0.500000 0.000000 31.95518 SMTRY3 9 0.000000 0.000000 1.000000 39.09767 SMTRY1 10 -0.500000 0.866025 0.000000 55.34800 SMTRY2 10 0.866025 0.500000 0.000000 31.95518 SMTRY3 10 0.000000 0.000000 -1.000000 39.09767 SMTRY1 11 1.000000 0.000000 0.000000 55.34800 SMTRY2 11 0.000000 -1.000000 0.000000 31.95518 SMTRY3 11 0.000000 0.000000 -1.000000 39.09767 SMTRY1 12 -0.500000 -0.866025 0.000000 55.34800 SMTRY2 12 -0.866025 0.500000 0.000000 31.95518 SMTRY3 12 0.000000 0.000000 -1.000000 39.09767 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 SMTRY2 13 0.000000 1.000000 0.000000 63.91037 SMTRY3 13 0.000000 0.000000 1.000000 78.19533 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 SMTRY2 14 0.866025 -0.500000 0.000000 63.91037 SMTRY3 14 0.000000 0.000000 1.000000 78.19533 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 SMTRY2 15 -0.866025 -0.500000 0.000000 63.91037 SMTRY3 15 0.000000 0.000000 1.000000 78.19533 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 SMTRY2 16 0.866025 0.500000 0.000000 63.91037 SMTRY3 16 0.000000 0.000000 -1.000000 78.19533 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 SMTRY2 17 0.000000 -1.000000 0.000000 63.91037 SMTRY3 17 0.000000 0.000000 -1.000000 78.19533 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 SMTRY2 18 -0.866025 0.500000 0.000000 63.91037 SMTRY3 18 0.000000 0.000000 -1.000000 78.19533 REMARK: NULL BIOMOLECULE: 1 THIS ENTRY CONTAINS THE UNIQUE NON-CRYSTALLOGRAPHIC VIRAL REPEAT UNIT, WHICH CONSISTS OF 5 CHAIN(S). SEE FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). QUATERNARY STRUCTURE FOR THIS ENTRY: VIRUS GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, B, C, R, S BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -0.000007 -0.934176 0.356813 0.00000 BIOMT2 2 -0.356827 0.333330 0.872672 0.00000 BIOMT3 2 -0.934180 -0.127331 -0.333324 0.00000 BIOMT1 3 0.809013 -0.110269 0.577340 0.00000 BIOMT2 3 -0.467093 0.475679 0.745350 0.00000 BIOMT3 3 -0.356826 -0.872687 0.333341 0.00000 BIOMT1 4 0.500003 -0.866020 -0.000003 0.00000 BIOMT2 4 -0.645495 -0.372676 -0.666658 0.00000 BIOMT3 4 0.577363 0.333334 -0.745361 0.00000 BIOMT1 5 0.499998 -0.645498 0.577338 0.00000 BIOMT2 5 -0.866031 -0.372681 0.333333 0.00000 BIOMT3 5 0.000004 -0.666675 -0.745351 0.00000 BIOMT1 6 0.309020 -0.755754 -0.577352 0.00000 BIOMT2 6 -0.755766 -0.563664 0.333336 0.00000 BIOMT3 6 -0.577350 0.333329 -0.745356 0.00000 BIOMT1 7 0.809022 -0.467080 -0.356818 0.00000 BIOMT2 7 -0.110259 0.475688 -0.872669 0.00000 BIOMT3 7 0.577360 0.745362 0.333326 0.00000 BIOMT1 8 0.809023 0.110276 -0.577347 0.00000 BIOMT2 8 -0.467084 -0.475684 -0.745347 0.00000 BIOMT3 8 -0.356817 0.872684 -0.333338 0.00000 BIOMT1 9 0.309005 -0.178418 0.934164 0.00000 BIOMT2 9 0.178413 0.975684 0.127318 0.00000 BIOMT3 9 -0.934180 0.127320 0.333344 0.00000 BIOMT1 10 0.809013 0.467090 0.356821 0.00000 BIOMT2 10 0.110270 0.475686 -0.872672 0.00000 BIOMT3 10 -0.577350 0.745363 0.333336 0.00000 BIOMT1 11 -0.500000 -0.866025 0.000000 0.00000 BIOMT2 11 0.866025 -0.500000 0.000000 0.00000 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 BIOMT1 12 0.309025 0.178416 -0.934162 0.00000 BIOMT2 12 0.178407 -0.975685 -0.127327 0.00000 BIOMT3 12 -0.934180 -0.127331 -0.333324 0.00000 BIOMT1 13 0.000008 -0.356815 -0.934162 0.00000 BIOMT2 13 0.934172 -0.333335 0.127316 0.00000 BIOMT3 13 -0.356826 -0.872687 0.333341 0.00000 BIOMT1 14 0.309013 0.755757 0.577344 0.00000 BIOMT2 14 0.755763 -0.563657 0.333326 0.00000 BIOMT3 14 0.577363 0.333334 -0.745361 0.00000 BIOMT1 15 0.500005 0.645500 -0.577344 0.00000 BIOMT2 15 0.866026 -0.372677 0.333323 0.00000 BIOMT3 15 0.000004 -0.666675 -0.745351 0.00000 BIOMT1 16 0.500002 0.866024 -0.000001 0.00000 BIOMT2 16 0.645502 -0.372670 -0.666669 0.00000 BIOMT3 16 -0.577350 0.333329 -0.745356 0.00000 BIOMT1 17 -0.309024 -0.178418 0.934162 0.00000 BIOMT2 17 0.755763 -0.642347 0.127321 0.00000 BIOMT3 17 0.577360 0.745362 0.333326 0.00000 BIOMT1 18 -0.000005 0.356816 0.934163 0.00000 BIOMT2 18 0.934176 0.333344 -0.127323 0.00000 BIOMT3 18 -0.356817 0.872684 -0.333338 0.00000 BIOMT1 19 -0.309013 -0.755758 -0.577343 0.00000 BIOMT2 19 0.178400 -0.642356 0.745350 0.00000 BIOMT3 19 -0.934180 0.127320 0.333344 0.00000 BIOMT1 20 -0.500003 -0.645501 0.577345 0.00000 BIOMT2 20 0.645490 0.166669 0.745352 0.00000 BIOMT3 20 -0.577350 0.745363 0.333336 0.00000 BIOMT1 21 -0.500000 0.866025 0.000000 0.00000 BIOMT2 21 -0.866025 -0.500000 0.000000 0.00000 BIOMT3 21 0.000000 0.000000 1.000000 0.00000 BIOMT1 22 -0.309018 0.755760 0.577349 0.00000 BIOMT2 22 0.178420 0.642355 -0.745345 0.00000 BIOMT3 22 -0.934180 -0.127331 -0.333324 0.00000 BIOMT1 23 -0.809021 0.467084 0.356822 0.00000 BIOMT2 23 -0.467079 -0.142344 -0.872666 0.00000 BIOMT3 23 -0.356826 -0.872687 0.333341 0.00000 BIOMT1 24 -0.809016 0.110263 -0.577341 0.00000 BIOMT2 24 -0.110268 0.936333 0.333332 0.00000 BIOMT3 24 0.577363 0.333334 -0.745361 0.00000 BIOMT1 25 -1.000003 -0.000002 0.000006 0.00000 BIOMT2 25 0.000005 0.745358 -0.666656 0.00000 BIOMT3 25 0.000004 -0.666675 -0.745351 0.00000 BIOMT1 26 -0.809022 -0.110270 0.577353 0.00000 BIOMT2 26 0.110264 0.936334 0.333333 0.00000 BIOMT3 26 -0.577350 0.333329 -0.745356 0.00000 BIOMT1 27 -0.499998 0.645498 -0.577344 0.00000 BIOMT2 27 -0.645504 0.166659 0.745348 0.00000 BIOMT3 27 0.577360 0.745362 0.333326 0.00000 BIOMT1 28 -0.809018 -0.467092 -0.356816 0.00000 BIOMT2 28 -0.467092 0.142340 0.872670 0.00000 BIOMT3 28 -0.356817 0.872684 -0.333338 0.00000 BIOMT1 29 0.000008 0.934176 -0.356821 0.00000 BIOMT2 29 -0.356813 -0.333328 -0.872668 0.00000 BIOMT3 29 -0.934180 0.127320 0.333344 0.00000 BIOMT1 30 -0.309010 0.178411 -0.934166 0.00000 BIOMT2 30 -0.755760 -0.642355 0.127320 0.00000 BIOMT3 30 -0.577350 0.745363 0.333336 0.00000 BIOMT1 31 -0.500000 0.866025 0.000000 0.00000 BIOMT2 31 0.866025 0.500000 0.000000 0.00000 BIOMT3 31 0.000000 0.000000 -1.000000 0.00000 BIOMT1 32 -0.309018 0.755760 0.577349 0.00000 BIOMT2 32 -0.178420 -0.642355 0.745345 0.00000 BIOMT3 32 0.934180 0.127331 0.333324 0.00000 BIOMT1 33 -0.809021 0.467084 0.356822 0.00000 BIOMT2 33 0.467079 0.142344 0.872666 0.00000 BIOMT3 33 0.356826 0.872687 -0.333341 0.00000 BIOMT1 34 -0.809016 0.110263 -0.577341 0.00000 BIOMT2 34 0.110268 -0.936333 -0.333332 0.00000 BIOMT3 34 -0.577363 -0.333334 0.745361 0.00000 BIOMT1 35 -1.000003 -0.000002 0.000006 0.00000 BIOMT2 35 -0.000005 -0.745358 0.666656 0.00000 BIOMT3 35 -0.000004 0.666675 0.745351 0.00000 BIOMT1 36 -0.809022 -0.110270 0.577353 0.00000 BIOMT2 36 -0.110264 -0.936334 -0.333333 0.00000 BIOMT3 36 0.577350 -0.333329 0.745356 0.00000 BIOMT1 37 -0.499998 0.645498 -0.577344 0.00000 BIOMT2 37 0.645504 -0.166659 -0.745348 0.00000 BIOMT3 37 -0.577360 -0.745362 -0.333326 0.00000 BIOMT1 38 -0.809018 -0.467092 -0.356816 0.00000 BIOMT2 38 0.467092 -0.142340 -0.872670 0.00000 BIOMT3 38 0.356817 -0.872684 0.333338 0.00000 BIOMT1 39 0.000008 0.934176 -0.356821 0.00000 BIOMT2 39 0.356813 0.333328 0.872668 0.00000 BIOMT3 39 0.934180 -0.127320 -0.333344 0.00000 BIOMT1 40 -0.309010 0.178411 -0.934166 0.00000 BIOMT2 40 0.755760 0.642355 -0.127320 0.00000 BIOMT3 40 0.577350 -0.745363 -0.333336 0.00000 BIOMT1 41 1.000000 0.000000 0.000000 0.00000 BIOMT2 41 0.000000 -1.000000 0.000000 0.00000 BIOMT3 41 0.000000 0.000000 -1.000000 0.00000 BIOMT1 42 -0.000007 -0.934176 0.356813 0.00000 BIOMT2 42 0.356827 -0.333330 -0.872672 0.00000 BIOMT3 42 0.934180 0.127331 0.333324 0.00000 BIOMT1 43 0.809013 -0.110269 0.577340 0.00000 BIOMT2 43 0.467093 -0.475679 -0.745350 0.00000 BIOMT3 43 0.356826 0.872687 -0.333341 0.00000 BIOMT1 44 0.500003 -0.866020 -0.000003 0.00000 BIOMT2 44 0.645495 0.372676 0.666658 0.00000 BIOMT3 44 -0.577363 -0.333334 0.745361 0.00000 BIOMT1 45 0.499998 -0.645498 0.577338 0.00000 BIOMT2 45 0.866031 0.372681 -0.333333 0.00000 BIOMT3 45 -0.000004 0.666675 0.745351 0.00000 BIOMT1 46 0.309020 -0.755754 -0.577352 0.00000 BIOMT2 46 0.755766 0.563664 -0.333336 0.00000 BIOMT3 46 0.577350 -0.333329 0.745356 0.00000 BIOMT1 47 0.809022 -0.467080 -0.356818 0.00000 BIOMT2 47 0.110259 -0.475688 0.872669 0.00000 BIOMT3 47 -0.577360 -0.745362 -0.333326 0.00000 BIOMT1 48 0.809023 0.110276 -0.577347 0.00000 BIOMT2 48 0.467084 0.475684 0.745347 0.00000 BIOMT3 48 0.356817 -0.872684 0.333338 0.00000 BIOMT1 49 0.309005 -0.178418 0.934164 0.00000 BIOMT2 49 -0.178413 -0.975684 -0.127318 0.00000 BIOMT3 49 0.934180 -0.127320 -0.333344 0.00000 BIOMT1 50 0.809013 0.467090 0.356821 0.00000 BIOMT2 50 -0.110270 -0.475686 0.872672 0.00000 BIOMT3 50 0.577350 -0.745363 -0.333336 0.00000 BIOMT1 51 -0.500000 -0.866025 0.000000 0.00000 BIOMT2 51 -0.866025 0.500000 0.000000 0.00000 BIOMT3 51 0.000000 0.000000 -1.000000 0.00000 BIOMT1 52 0.309025 0.178416 -0.934162 0.00000 BIOMT2 52 -0.178407 0.975685 0.127327 0.00000 BIOMT3 52 0.934180 0.127331 0.333324 0.00000 BIOMT1 53 0.000008 -0.356815 -0.934162 0.00000 BIOMT2 53 -0.934172 0.333335 -0.127316 0.00000 BIOMT3 53 0.356826 0.872687 -0.333341 0.00000 BIOMT1 54 0.309013 0.755757 0.577344 0.00000 BIOMT2 54 -0.755763 0.563657 -0.333326 0.00000 BIOMT3 54 -0.577363 -0.333334 0.745361 0.00000 BIOMT1 55 0.500005 0.645500 -0.577344 0.00000 BIOMT2 55 -0.866026 0.372677 -0.333323 0.00000 BIOMT3 55 -0.000004 0.666675 0.745351 0.00000 BIOMT1 56 0.500002 0.866024 -0.000001 0.00000 BIOMT2 56 -0.645502 0.372670 0.666669 0.00000 BIOMT3 56 0.577350 -0.333329 0.745356 0.00000 BIOMT1 57 -0.309024 -0.178418 0.934162 0.00000 BIOMT2 57 -0.755763 0.642347 -0.127321 0.00000 BIOMT3 57 -0.577360 -0.745362 -0.333326 0.00000 BIOMT1 58 -0.000005 0.356816 0.934163 0.00000 BIOMT2 58 -0.934176 -0.333344 0.127323 0.00000 BIOMT3 58 0.356817 -0.872684 0.333338 0.00000 BIOMT1 59 -0.309013 -0.755758 -0.577343 0.00000 BIOMT2 59 -0.178400 0.642356 -0.745350 0.00000 BIOMT3 59 0.934180 -0.127320 -0.333344 0.00000 BIOMT1 60 -0.500003 -0.645501 0.577345 0.00000 BIOMT2 60 -0.645490 -0.166669 -0.745352 0.00000 BIOMT3 60 0.577350 -0.745363 -0.333336 0.00000

-
Components

#1: RNA chain 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP*AP*AP*GP*AP*CP*AP*GP*CP*AP*U)-3'


Mass: 6391.863 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Coat protein


Mass: 13711.505 Da / Num. of mol.: 3 / Mutation: N87S, E89K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MS2 Coat protein in 1.25% or 1.5% PEG 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
20.4M SODIUM PHOSPHATE BUFFER11
3water11
4PEG 800012
50.4M SODIUM PHOSPHATE BUFFER12
6water12

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 228202 / Num. obs: 147903 / % possible obs: 64.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 0.212 / Net I/σ(I): 2.8
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.461 / % possible all: 65.2

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B ...Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B chain instead of the chain used for the actual refinement has been included so that the protein-RNA interactions between the AB dimer and the R chain RNA are clear without generating the NCS symmetry related 'B' chain.
RfactorNum. reflectionSelection details
Rfree0.203 5919 RANDOM
Rwork0.197 --
all0.197 228202 -
obs0.197 147903 -
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 258 0 119 3263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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