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cd00403: Ribosomal_L1 
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Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Statistics
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PSSM-Id: 238235
View PSSM: cd00403
Aligned: 212 rows
Threshold Bit Score: 80.3059
Threshold Setting Gi: 71666724
Created: 6-Mar-2002
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
Hierarchy
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mRNA/rRNA
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:mRNA/rRNA interface [nucleic acid binding site]
Evidence:
  • Comment:L1 recognizes the same structural motif in both rRNA and mRNA, using the same RNA binding site for both.
  • Structure:1U63_A: Methanococcus jannaschii L1 forms an interface with mRNA fragments (1U63_B/1U63_D), defined using 3.5 A contacts.
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  • Structure:1MZP_A: Sulfolobus acidocaldarius L1 forms an interface with 23S rRNA (1MZP_B), defined using 3.5 A contacts.
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  • Structure:2HGU_C: Thermus thermophilus L1 forms an interface with 23S rRNA (2HGU_A), defined using 3.5 A contacts.
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  • Comment:L1 has been observed in both open and closed conformations. Because of the hinge motion between the two domains, a slightly different set of residues is within 3.5 A proximity to 23S rRNA in 1MZP and 2HGU.

cd00403 is part of a hierarchy of related CD models.
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cd00403 is a member of the superfamily cl00322.
cd00403:Ribosomal_L12NOQ G85086835227636771021895531171147904776220018854727121667084051572318387105611567546105738231152422482349746166360018710282346747693966818615717489902106402914551000914616240413812068419336371080735757563811917080547042821911486539969825461212018510474615604994367541056111065816502574911165031957100617850552708152214752180573914780002111546538911605806265304974663630941454792891461858626813036171666724245828741088758074722611911130656668533951118097676149631830525455101263348771158996536321843495270434519083950312047504232831261363311464163956848353914923597763229131561159175028896345185938503026415042424512613681714641964614924517212346962517561330674748691773784391091734110768302504179691MZP A118431765124028450126465990118194956154241961119719141181613881263533041CJS A1U63 A39147044432882886019531988729839147051991838891773885110622965116754718157901961608148948477510126008616124805683156087404632032149645081156113472449859584952435150413793146421089150866550684913805055057577110773997623346123109850912936790247690301459111056075154285416502596041165093707106292691219008145490193146184970564165435857883258419223306891191255556721160608945269849114828410913506243230758417104163602937171344405120989015229443114654923046813114021280912224093791300026883054252792524216122156180022GYA 2946765172167233127903947335200037179643511651497125166475456446623330143314632670810875692339576595508760031215432947822043811477890010783733813880190284936801245144532HGU C333014741831139810880498413943853476261520147669525216460553454021894502268838167909497170513275729841941350682196990292655347868995451582848147458974148377349263237042561511397218521971330732448295149177087912006571491989121503857501538918632NOQ G85086835227636771021895531171147904776220018854727121667084051572318387105611567546105738231152422482349746166360018710282346747693966818615717489902106402914551000914616240413812068419336371080735757563811917080547042821911486539969825461212018510474615604994367541056111065816502574911165031957100617850552708152214752180573914780002111546538911605806265304974663630941454792891461858626813036171666724245828741088758074722611911130656668533951118097676149631830525455101263348771158996536321843495270434519083950312047504232831261363311464163956848353914923597763229131561159175028896345185938503026415042424512613681714641964614924517212346962517561330674748691773784391091734110768302504179691MZP A118431765124028450126465990118194956154241961119719141181613881263533041CJS A1U63 A39147044432882886019531988729839147051991838891773885110622965116754718157901961608148948477510126008616124805683156087404632032149645081156113472449859584952435150413793146421089150866550684913805055057577110773997623346123109850912936790247690301459111056075154285416502596041165093707106292691219008145490193146184970564165435857883258419223306891191255556721160608945269849114828410913506243230758417104163602937171344405120989015229443114654923046813114021280912224093791300026883054252792524216122156180022GYA 2946765172167233127903947335200037179643511651497125166475456446623330143314632670810875692339576595508760031215432947822043811477890010783733813880190284936801245144532HGU C33301474183113981088049841394385347626152014766952521646055345402189450226883816790949717051327572984194135068219699029265534786899545158284814745897414837734926323704256151139721852197133073244829514917708791200657149198912150385750153891863
cd00403 Sequence Cluster
cd00403 Sequence Cluster
Sub-family Hierarchy
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CD Hierarchy
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                              ###  # # # #                                              
1MZP_A         8 LIEALKLALStey------nvkRNFTQSVEIILTFKgidxkkgDLKLREIVP----LPKQPs--KAKRVLVVps-seQLE 74
1U63_A         6 LLQAVKEAREla--------kpRNFTQSFEFIATLKeidxrkpENRIKTEVV----LPHGRg--KEAKIAVIgt-gdLAK 70
gi 17561330  176 APQAISALKKffaekn-ekslfPDIDYALNLSVTYKksa--itTDQGKIKIK----LPHSTrniNNTSVCVImp-dlDQS 247
gi 17737843   99 VQEAIQCHREthhp-----smyNVPNAPLNLDIELNmqa--ekITRFVDNFQrmamIPHKFdhgEERKIIVFtkgnnEVL 171
gi 24582874  277 VCAALKSVVSeevek--kkntsIFSDYRYVLQVCSYki---psCPKRMVKLN----LKHSLv-gKDDDVALIvp-dlQRG 345
gi 67474869   52 ILKTIRAIKQyndyetknsgitSLFNTDKQLQIKFDil----kEPRYNPHIDfl-tVPHPFy--NKRSICLIca-npKSY 123
gi 68130361   19 ASETAAQPSGndvddl-fapvrESNNVPVDVQIAFLaa---paAHRVPLYFV----VPHET---VSGTLCLItp-ppQRK 86
gi 71666724   27 ENDILGDLFSps---------tQTHFRSVDVEVTFLls---pvAHRVPLYFT----VPHEV---LPGTVCLVtp-paQRK 86
gi 91091734   95 LVEAIKNHREthhp-----dmyNEPGASLLVRIELNmqg--ekATRFVDDFTrivpIPFKFehgEERPIIAFaktgsAQK 167
gi 108875807 137 IKTALKACKKaldegfdqkknlFGEDLKYGLQIACVki---pdVPSRNCRVQ----LPNAIy-kKGDDICLIvk-dlERG 207
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1MZP_A        75 YAKka-------------------------sPKVVItrEELQKLQGQkrpvkklarQNEWFLInq-esXALAGRILGPAL 128
1U63_A        71 QAEel-------------------------gLTVIRk-EEIEELGKNkrklrkiakAHDFFIAqa-dlXPLIGRYXGVIL 123
gi 17561330  248 DAAkrdfdvekqsrewaekievdhgltsahiAKILTk-REVERIAHTykdkrslasTYDVFLSdg-rvYNSVKSFLGKEF 325
gi 17737843  172 EARea-------------------------gASLVGg-VELIKDITSgel---llsDYQYVIAh----PNILAELVALRG 218
gi 24582874  346 AKFdydptkqhyed-------mlreagvkqrLTVVPf-NQLRNEMGSfeakrkflnSYDYLLCdg-rlSGQATAFLGKNT 416
gi 67474869  124 MKEkvaka-------------------gvhvDKIISt-KQIRERYTTfeaqdelmkRYDVFLVeirvcHLISILFLGRIR 183
gi 68130361   87 YKDlvfalsed------------gdavakrvRRVIDs-KKLAAKVTDpvavrsfakSYDHFIVy---gLTNYPRQLTGEF 150
gi 71666724   87 YKDkilrlsee------------gnsvaqrvKKVIDt-KKLSTKFVDpvavralanSFDHFILf---gVKKYPPQLTGEF 150
gi 91091734  168 EALna-------------------------gAQLAGg-VDLIKQVQNgav---slqNFKFVIAh----PDILPELVALRG 214
gi 108875807 208 RKQeheetlsfwnd-------klrelnidfiTQVIPf-RQLKQDYREyemklklvhRFDRFLVda-riNGHVYNFLGNNF 278
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                  #  # #                                
1MZP_A       129 GP--RGKFPTPlpn--taDISEYINRFKr-----SVLVKTKDQp-QVQVFIGTEDXKPEDLAENAIAVLNAIEnkak--- 195
1U63_A       124 GP--RGKXPKPvpa--naNIKPLVERLKk-----TVVINTRDKp-YFQVLVGNEKXTDEQIVDNIEAVLNVVAkkye--- 190
gi 17561330  326 YRahKCPLPFVyq----kPISTAIENALr-----TVVYPLRRYmvRSCVNVGHLGQSSADLKENIDTVLEKIAskcp--- 393
gi 17737843  219 LM--KRKFPNPksetlgtNLAEMIVKFSsgisysAAKDEYQQNfgLITASVGTLDMDVQKLEENIKFLLQDINtmrpk-- 294
gi 24582874  417 QKp-RNVLHSLrlskdndKLPQEVTRALt----rTAFRQLSKGd-LIAVPVGNHEITAEQLAENILLVIKQLQevyp--- 487
gi 67474869  184 SK--NLFIPVFcg---kySIKREIEKAIe-----SIPFTPLRSa-YLSIPFGVLSQSDDDLADNFIALTKQASecmy--- 249
gi 68130361  151 LE--HRKVPAWvns--kgKFPEKLRKAV------HTVVVSRRGdnQVTCRVGHTGLSTQELVENIIAFLDKFVkhpdgvp 220
gi 71666724  151 LG--HQKSPVWvsr--rgGLREKLLSAVk-----TVVFQRRGNs-AVTCRIGHTGLLLEQLHENLHSFLAQMTshaqaat 220
gi 91091734  215 LM--KRRFPNPkmgtldvDLGAVAERFVngisytAKKDEYEKDfgLIETVIGSLDMDVEHLEGNFGALVKDVYsmrpk-- 290
gi 108875807 279 IR--RCKNPTPvildkdeKIVKSLNKALg----rVTYKQTNTGr-ITEIQFATHKMPLEKAVENAESLLQTMKtqyp--- 348
                        250       260
                 ....*....|....*....|....
Feature 1                         ## #   
1MZP_A       196 --vetNLRNIYVKTt--XGKAVKV 215
1U63_A       191 -kglyHIKDAYVKLt--XGPAVKV 211
gi 17561330  394 -ggfaNIRSIYLGAs-dGKPSLPI 415
gi 17737843  295 -regrFITRVLLKSp-pSSEQLKI 316
gi 24582874  488 -gglaNIRSMYLKIditGTSALPL 510
gi 67474869  250 -egsdNITQIQVNVk-gGSVAFPV 271
gi 68130361  221 lknilHIRVAATSTn-sKRVGLPI 243
gi 71666724  221 pqdilHIRVAGTNTd-gRRAGLPI 243
gi 91091734  291 -rqgdFISRCLLVSp-pSSEKFKV 312
gi 108875807 349 -ggwrNIRTVYLKPmtdIQLTFPL 371

Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
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Conserved site includes 13 residues -Click on image for an interactive view with Cn3D