PDB entry 2vqf

View 2vqf on RCSB PDB site
Description: modified uridines with c5-methylene substituents at the first position of the tRNA anticodon stabilize u-g wobble pairing during decoding
Class: ribosome
Keywords: tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation, coiled coil, paromomycin, tRNA, zinc, mRNA, cmo5u, ribosome, RNA-binding, modifiactions, ribosomal protein, ribonucleoprotein
Deposited on 2008-03-14, released 2008-04-29
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.223
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 16s rRNA
    Species: Thermus thermophilus [TaxId:300852]
  • Chain 'B':
    Compound: 30S ribosomal protein S2
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfb1
  • Chain 'C':
    Compound: 30S ribosomal protein S3
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfd1
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfe1
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqff1
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfg1
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfh1
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfi1
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfj1
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfk1
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfl1
  • Chain 'M':
    Compound: 30S ribosomal protein S13
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfm1
  • Chain 'N':
    Compound: 30s ribosomal protein s14 type z
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfn1
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfo1
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfp1
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfq1
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfr1
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfs1
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqft1
  • Chain 'U':
    Compound: 30S ribosomal protein Thx
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2vqfu1
  • Chain 'X':
    Compound: 5'-r(*up*up*gp*ap*ap*ap)-3'
    Species: Thermus thermophilus [TaxId:300852]
  • Chain 'Y':
    Compound: 5'-r(*gp*cp*ap*up*gp*cp*u*tm2p*ap*ap*ap *ap*cp*ap*up*gp*c)-3'
    Species: Thermus thermophilus [TaxId:300852]
  • Heterogens: PAR, MG, ZN, K

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vqfB (B:)
    mpveitvkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfied
    lamrggtilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelea
    lfaspeieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearkl
    fipvialadtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq
    eaeatetpegesevea
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfB (B:)
    vkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfiedlamrgg
    tilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelealfaspe
    ieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearklfipvia
    ladtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvqe
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2vqfD (D:)
    mgryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlre
    kqklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarql
    vrhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldveg
    mkgkflrlpdredlalpvneqlviefysr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfD (D:)
    gryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlrek
    qklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarqlv
    rhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldvegm
    kgkflrlpdredlalpvneqlviefysr
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2vqfE (E:)
    mpetdfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagy
    yarrnmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdilt
    kelgsrnpiniayatmealrqlrtkadverlrkgeahaqaqg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfE (E:)
    dfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagyyarr
    nmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdiltkelg
    srnpiniayatmealrqlrtkadverlrkge
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vqfF (F:)
    mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf
    lwyqvempedrvndlarelrirdnvrrvmvvksqepflana
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2vqfG (G:)
    marrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplk
    vfkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavri
    ahelmdaaegkggavkkkedvermaeanrayahyrw
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfG (G:)
    arrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplkv
    fkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavria
    helmdaaegkggavkkkedvermaeanrayahyrw
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vqfH (H:)
    mltdpiadmltrirnatrvykestdvpasrfkeeilrilaregfikgyervdvdgkpylr
    vylkygprrqgpdprpeqvihhirriskpgrrvyvgvkeiprvrrglgiailstskgvlt
    drearklgvggelicevw
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2vqfI (I:)
    meqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfd
    ayitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkar
    rapqyskr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfI (I:)
    eqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfda
    yitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkarr
    apqyskr
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2vqfJ (J:)
    mpkiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsr
    ehfelrthnrlvdiinpnrktieqlmtldlptgveieiktvgggr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfJ (J:)
    kiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsreh
    felrthnrlvdiinpnrktieqlmtldlptgveieiktv
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2vqfK (K:)
    makkpskkkvkrqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpya
    aqlaaldaakkamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcr
    pkkkfrkas
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfK (K:)
    krqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpyaaqlaaldaak
    kamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcrpkkkfrkas
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2vqfL (L:)
    mvalptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrl
    tsgyevtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrsky
    gtkkpkeaaktaakk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfL (L:)
    ptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrltsgy
    evtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskygtkk
    pkeaa
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >2vqfM (M:)
    mariagveiprnkrvdvaltyiygigkarakealektginpatrvkdlteaevvrlreyv
    entwklegelraevaanikrlmdigcyrglrhrrglpvrgqrtrtnartrkgprktvagk
    kkaprk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfM (M:)
    ariagveiprnkrvdvaltyiygigkarakealektginpatrvkdlteaevvrlreyve
    ntwklegelraevaanikrlmdigcyrglrhrrglpvrgqrtrtnartrkgprktvagkk
    kaprk
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >2vqfN (N:)
    markaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkas
    w
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfN (N:)
    arkaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkasw
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >2vqfO (O:)
    mpitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmv
    gqrrrllrylqredperyralieklgirg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfO (O:)
    pitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmvg
    qrrrllrylqredperyralieklgirg
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >2vqfP (P:)
    mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
    svgaqptdtarrllrqagvfrqearega
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfP (P:)
    mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
    svgaqptdtarrllrqagvfrqea
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >2vqfQ (Q:)
    mpkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveii
    esrpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfQ (Q:)
    pkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveiie
    srpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >2vqfR (R:)
    mstknakpkkeaqrrpsrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsg
    keqrilaktikrarilgllpfteklvrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfR (R:)
    psrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsgkeqrilaktikrari
    lgllpfteklvrk
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >2vqfS (S:)
    mprslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpv
    yitenmvghklgefaptrtyrghgkeakatkkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfS (S:)
    prslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpvy
    itenmvghklgefaptrtyrg
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >2vqfT (T:)
    maqkkpkrnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkae
    slidkaakgstlhknaaarrksrlmrkvrqlleaagapliggglsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfT (T:)
    rnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkaeslidkaa
    kgstlhknaaarrksrlmrkvrqlleaagapliggglsa
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >2vqfU (U:)
    mgkgdrrtrrgkiwrgtygkyrprkkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vqfU (U:)
    gkgdrrtrrgkiwrgtygkyrprkk
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.