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PDB | 1RY1 | Structure of the signal recognition particle interacting with the elongation-arrested ribosome

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Internal ID
21083
PDB Entry ID
1RY1
Title
Structure of the signal recognition particle interacting with the elongation-arrested ribosome
Authors
Halic, M.,Becker, T.,Pool, M.R.,Spahn, C.M.,Grassucci, R.A.,Frank, J.,Beckmann, R.
Primary Citation
AuthorsHalic, M., Becker, T., Pool, M.R., Spahn, C.M., Grassucci, R.A., Frank, J., Beckmann, R.
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome
JournalNature, v.427, pp.808 - 814, 2004
AbstractView
Pubmed14985753
DOI10.1038/nature02342
 
History
Deposition: 2003-12-19Release: 2004-04-20Last Modified: 2009-02-24
Experimental Method
TypeELECTRON MICROSCOPY
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
12.00n/an/an/a
Unit Cell
Length [Å]abc
Angles [°]alphabetagamma
Molecular Description
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PolymerMoleculeMutationFragmentChainsEC NumberOther details
1ALU DOMAIN (RNA FRAGMENTS)E
2ALU DOMAIN (SRP9, SRP14 + RNA)A
3fragment of 7S RNAM
4RNA (31-MER)N
5RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')O
6RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')P
7RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')Q
8RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')R
9PROTEIN (Signal recognition particle 9 kDa protein)C
10PROTEIN (Signal recognition particle 14 kDa protein)D
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Functional Class
Source
PolymerScientific NameCommon NameExpression System
9Homo sapienshumann/a
10Homo sapienshumann/a
11Homo sapienshumann/a
12Thermus aquaticusn/a
13Mus musculushouse mousen/a
14Tursiops truncatusbottlenosed dolphinn/a
Related PDB Entries
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
CCCCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATEC9H13N3O10P2[View][View]
GDPGUANOSINE-5'-DIPHOSPHATEC10H15N5O11P2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSLATION
Textsignal recognition particle, RNA binding, TRANSLATION
 
Polymeric Molecules
Chain E
DescriptionALU DOMAIN (RNA FRAGMENTS)
Polymer typepolyribonucleotide
Formula Weight16277.7
Source Methodsynthetic
Entity Name Sysn/a
 
Chain A
DescriptionALU DOMAIN (SRP9, SRP14 + RNA)
Polymer typepolyribonucleotide
Formula Weight41567.0
Source Methodsynthetic
Entity Name Sysn/a
 
Chain M
Descriptionfragment of 7S RNA
Polymer typepolyribonucleotide
Formula Weight8784.3
Source Methodsynthetic
Entity Name Sysn/a
 
Chain N
DescriptionRNA (31-MER)
Polymer typepolyribonucleotide
Formula Weight9807.9
Source Methodsynthetic
Entity Name Sysn/a
 
Chain O
DescriptionRNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
Polymer typepolyribonucleotide
Formula Weight7695.6
Source Methodsynthetic
Entity Name Sysn/a
 
Chain P
DescriptionRNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
Polymer typepolyribonucleotide
Formula Weight6325.9
Source Methodsynthetic
Entity Name Sysn/a
 
Chain Q
DescriptionRNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
Polymer typepolyribonucleotide
Formula Weight3844.3
Source Methodsynthetic
Entity Name Sysn/a
 
Chain R
DescriptionRNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')
Polymer typepolyribonucleotide
Formula Weight3804.3
Source Methodsynthetic
Entity Name Sysn/a
 
Chain C
DescriptionPROTEIN (Signal recognition particle 9 kDa protein)
Polymer typepolypeptide
Formula Weight9996.6
Source Methodgenetically manipulated
Entity NameSRP9
Entity Name Sysn/a
 
Chain D
DescriptionPROTEIN (Signal recognition particle 14 kDa protein)
Polymer typepolypeptide
Formula Weight12114.3
Source Methodgenetically manipulated
Entity NameSRP14, 18 kDa ALU RNA binding protein
Entity Name Sysn/a
 
Chain B
DescriptionPROTEIN (Signal recognition particle 19 kDa protein)
Polymer typepolypeptide
Formula Weight12561.8
Source Methodgenetically manipulated
Entity NameSRP19
Entity Name Sysn/a
 
Chain U
DescriptionSignal recognition particle protein
Polymer typepolypeptide
Formula Weight32472.8
Source Methodgenetically manipulated
Entity NameFifty-four homolog
Entity Name Sysn/a
 
Chain W
DescriptionSignal recognition particle 54 kDa protein
Polymer typepolypeptide
Formula Weight12473.5
Source Methodgenetically manipulated
Entity NameSRP54
Entity Name Sysn/a
 
Chain S
DescriptionRhodopsin
Polymer typepolypeptide
Formula Weight2121.6
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
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EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anoyesn/aEpolyribonucleotiden/a
2n/anoyesn/aApolyribonucleotiden/a
3n/anonon/aMpolyribonucleotiden/a
4n/anonon/aNpolyribonucleotiden/a
5n/anonon/aOpolyribonucleotiden/a
6n/anonon/aPpolyribonucleotiden/a
7n/anonon/aQpolyribonucleotiden/a
8n/anonon/aRpolyribonucleotiden/a
9n/anonon/aCpolypeptide(L)n/a
10n/anonon/aDpolypeptide(L)n/a
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Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
CCCCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATEC9H13N3O10P2385.163View
GDPGUANOSINE-5'-DIPHOSPHATEC10H15N5O11P2443.203View
Natural/Genetically Modified Source
Common Namehuman
Scientific NameHomo sapiens
Source GenusHomo
GeneSRP9
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namehuman
Scientific NameHomo sapiens
Source GenusHomo
GeneSRP14
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namehuman
Scientific NameHomo sapiens
Source GenusHomo
GeneSRP19
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Scientific NameThermus aquaticus
Source GenusThermus
GeneFFH
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namehouse mouse
Scientific NameMus musculus
Source GenusMus
GeneSRP54
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namebottlenosed dolphin
Scientific NameTursiops truncatus
Source GenusTursiops
GeneRHO
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
Refinement Statistics
Structure Solution Methodn/a
Resolution (High)12.00
Resolution (Low)n/a
Cut-off Sigma (F)n/a
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free) n/a
Percent Reflections (Observed)n/a
R-Factor (All)n/a
R-Factor (Observed)n/a
R-Workn/a
R-Freen/a
R-Free Selection Detailsn/a
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Valuen/a
Anisotropic B[1][1]n/a
Anisotropic B[1][2]n/a
Anisotropic B[1][3]n/a
Anisotropic B[2][2]n/a
Anisotropic B[2][3]n/a
Anisotropic B[3][3]n/a
 
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms5335
Nucleic Acid Atoms6459
Heterogen Atoms0
Solvent Atoms0
 
Sequence Chain
E
Sequence
 1   GGGCCGGGCG  CGGUGGCGCG  CGCCUGUAGU  CCCAGCUACU  CGGGAGGCUC  

Sequence Chain
A
Sequence
  1   GACACUAAGU  UCGGCAUCAA  UAUGGUGACC  UCCCGGGAGC  GGGGGACCAC  CAGGUUGCCU

 61   AAGGAGGGGU  GAACCGGCCC  AGGUCGGAAA  CGGAGCAGGU  CAAAACUCCC  GUGCUGAUCA

121   GUAGUGUC  

Sequence Chain
M
Sequence
 1   AGGCUGGAGG  AUCGCUUGAG  UCCAGGA  

Sequence Chain
N
Sequence
 1   CCUGUGCAAC  AUAGCGAGAC  CCCGUCUCUU  U  

Sequence Chain
O
Sequence
 1   GUUCUGGGCU  GUAGUGCGCU  AUGC  

Sequence Chain
P
Sequence
 1   CAAUAGCCAC  UGCACUCCAG    

Sequence Chain
Q
Sequence
 1   CGAUCGGGUG  UC  

Sequence Chain
R
Sequence
 1   AUCGCGCCUG  UG  

Sequence Chain
C
Sequence
 1   PQYQTWEEFS  RAAEKLYLAD  PMKARVVLKY  RHSDGNLCVK  VTDDLVCLVY  KTDQAQDVKK

61   IEKFHSQLMR  LMVAKEARNV  TMETE  

Sequence Chain
D
Sequence
  1   VLLESEQFLT  ELTRLFQKCR  TSGSVYITLK  KYDGRTKPIP  KKGTVEGFEP  ADNKCLLRAT

 61   DGKKKISTVV  SSKEVNKFQM  AYSNLLRANM  DGLKKRDKKN  KTKKTK  

Sequence Chain
B
Sequence
  1   MRFICIYPAY  LNNKKTIAEG  RRIPISKAVE  NPTATEIQDV  CSAVGLNVFL  EKNKMYSREW

 61   NRDVQYRGRV  RVQLKQEDGS  LCLVQFPSRK  SVMLYAAEMI  PKLKTRTQ  

Sequence Chain
U
Sequence
  1   MFQQLSARLQ  EAIGRLRGRG  RITEEDLKAT  LREIRRALMD  ADVNLEVARD  FVERVREEAL

 61   GKQVLESLTP  AEVILATVYE  ALKEALGGEA  RLPVLKDRNL  WFLVGLQGSG  KTTTAAKLAL

121   YYKGKGRRPL  LVAADTQRPA  AREQLRLLGE  KVGVPVLEVM  DGESPESIRR  RVEEKARLEA

181   RDLILVDTAG  RLQIDEPLMG  ELARLKEVLG  PDEVLLVLDA  MTGQEALSVA  RAFDEKVGVT

241   GLVLTKLDGD  ARGGAALSAR  HVTGKPIYFA  GVSEKPEGLE  PFYPERLAGR  ILGMGD

Sequence Chain
W
Sequence
  1   QFTLRDMYEQ  FQNIMKMGPF  SQILGMIPGF  GTDFMSKGNE  QESMARLKKL  MTIMDSMNDQ

 61   ELDSTDGAKV  FSKQPGRIQR  VARGSGVSTR  DVQELLTQYT  KFAQMVKKM  

Sequence Chain
S
Sequence
 1   LGFPINFLTL  YVTVQHKK