PDB entry 3d5a

View 3d5a on RCSB PDB site
Description: Structural basis for translation termination on the 70S ribosome. This file contains the 30S subunit, release factor 1 (RF1), two tRNA, and mRNA molecules of one 70S ribosome. The entire crystal structure contains two 70S ribosomes as described in remark 400.
Class: ribosome
Keywords: Ribosome, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, Metal-binding, Zinc-finger, tRNA-binding, Protein biosynthesis
Deposited on 2008-05-16, released 2008-10-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3.21 Å
R-factor: 0.292
AEROSPACI score: 0.06 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 16s rRNA
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'B':
    Compound: 30S ribosomal protein S2
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ab1
  • Chain 'C':
    Compound: 30S ribosomal protein S3
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ad1
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ae1
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5af1
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ag1
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ah1
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ai1
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5aj1
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ak1
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5al1
  • Chain 'M':
    Compound: 30S ribosomal protein S13
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 30S ribosomal protein S14
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5an1
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ao1
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ap1
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5aq1
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ar1
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5as1
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5at1
  • Chain 'U':
    Compound: 30S ribosomal protein Thx
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5au1
  • Chain 'V':
    Compound: mRNA
  • Chain 'X':
    Compound: Peptide chain release factor 1
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: P and E-site tRNA(fMet)
    Species: Escherichia coli [TaxId:562]
  • Chain 'Z':
    Compound: P and E-site tRNA(fMet)
    Species: Escherichia coli [TaxId:562]
  • Heterogens: ZN, MG

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3d5aB (B:)
mpveitvkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfied
lamrggtilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelea
lfaspeieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearkl
fipvialadtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq
eaeatetpegesevea

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aB (B:)
vkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfiedlamrgg
tilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelealfaspe
ieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearklfipvia
ladtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3d5aD (D:)
mgryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlre
kqklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarql
vrhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldveg
mkgkflrlpdredlalpvneqlviefysr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aD (D:)
gryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlrek
qklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarqlv
rhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldvegm
kgkflrlpdredlalpvneqlviefysr

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3d5aE (E:)
mpetdfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagy
yarrnmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdilt
kelgsrnpiniayatmealrqlrtkadverlrkgeahaqaqg

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aE (E:)
dfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagyyarr
nmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdiltkelg
srnpiniayatmealrqlrtkadverlrkge

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3d5aF (F:)
mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf
lwyqvempedrvndlarelrirdnvrrvmvvksqepflana

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >3d5aG (G:)
marrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplk
vfkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavri
ahelmdaaegkggavkkkedvermaeanrayahyrw

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aG (G:)
arrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplkv
fkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavria
helmdaaegkggavkkkedvermaeanrayahyrw

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3d5aH (H:)
mltdpiadmltrirnatrvykestdvpasrfkeeilrilaregfikgyervdvdgkpylr
vylkygprrqgpdprpeqvihhirriskpgrrvyvgvkeiprvrrglgiailstskgvlt
drearklgvggelicevw

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >3d5aI (I:)
meqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfd
ayitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkar
rapqyskr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aI (I:)
eqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfda
yitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkarr
apqyskr

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >3d5aJ (J:)
mpkiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsr
ehfelrthnrlvdiinpnrktieqlmtldlptgveieiktvgggr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aJ (J:)
kiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsreh
felrthnrlvdiinpnrktieqlmtldlptgveieikt

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >3d5aK (K:)
makkpskkkvkrqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpya
aqlaaldaakkamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcr
pkkkfrkas

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aK (K:)
krqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpyaaqlaaldaak
kamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcrpkkkfrkas

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >3d5aL (L:)
malptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrlt
sgyevtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskyg
tkkpkeaaktaakk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aL (L:)
ptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrltsgy
evtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskygtkk
pkea

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >3d5aN (N:)
markaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkas
w

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aN (N:)
arkaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkasw

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >3d5aO (O:)
mpitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmv
gqrrrllrylqredperyralieklgirg

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aO (O:)
pitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmvg
qrrrllrylqredperyralieklgirg

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >3d5aP (P:)
mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
svgaqptdtarrllrqagvfrqearega

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aP (P:)
mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
svgaqptdtarrllrqagvfrqe

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >3d5aQ (Q:)
mpkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveii
esrpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aQ (Q:)
pkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveiie
srpiskrkrfrvlrlvesgrmdlvekylirrqnyqslsk

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >3d5aR (R:)
mstknakpkkeaqrrpsrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsa
keqrilaktikrarilgllpfteklvrk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aR (R:)
kakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsakeqrilaktikrarilgl
lpfteklvrk

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >3d5aS (S:)
mprslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpv
yitenmvghklgefaptrtyrghgkeakatkkk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aS (S:)
slkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpvyit
enmvghklgefaptrtyr

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >3d5aT (T:)
maqkkpkrnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkae
slidkaakgstlhknaaarrksrlmrkvrqlleaagapliggglsa

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aT (T:)
rnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkaeslidkaa
kgstlhknaaarrksrlmrkvrqlleaagapliggglsa

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >3d5aU (U:)
mgkgdrrtrrgkiwrgtygkyrprkkk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5aU (U:)
gkgdrrtrrgkiwrgtygkyrprk

  • Chain 'V':
    No sequence available.

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.