PDB entry 3d5c

View 3d5c 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 the second 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: d3d5cb1
  • 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: d3d5cd1
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ce1
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cf1
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cg1
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ch1
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ci1
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cj1
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ck1
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cl1
  • 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: d3d5cn1
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5co1
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cp1
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cq1
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cr1
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cs1
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5ct1
  • Chain 'U':
    Compound: 30S ribosomal protein Thx
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3d5cu1
  • 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: MG, ZN

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3d5cB (B:)
mpveitvkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfied
lamrggtilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelea
lfaspeieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearkl
fipvialadtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq
eaeatetpegesevea

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cB (B:)
vkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfiedlamrgg
tilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelealfaspe
ieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearklfipvia
ladtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3d5cD (D:)
mgryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlre
kqklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarql
vrhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldveg
mkgkflrlpdredlalpvneqlviefysr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cD (D:)
gryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlrek
qklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarqlv
rhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldvegm
kgkflrlpdredlalpvneqlviefysr

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3d5cE (E:)
mpetdfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagy
yarrnmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdilt
kelgsrnpiniayatmealrqlrtkadverlrkgeahaqaqg

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cE (E:)
dfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagyyarr
nmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdiltkelg
srnpiniayatmealrqlrtkadverlrkge

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3d5cF (F:)
mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf
lwyqvempedrvndlarelrirdnvrrvmvvksqepflana

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >3d5cG (G:)
marrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplk
vfkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavri
ahelmdaaegkggavkkkedvermaeanrayahyrw

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cG (G:)
arrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplkv
fkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavria
helmdaaegkggavkkkedvermaeanrayahyrw

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3d5cH (H:)
mltdpiadmltrirnatrvykestdvpasrfkeeilrilaregfikgyervdvdgkpylr
vylkygprrqgpdprpeqvihhirriskpgrrvyvgvkeiprvrrglgiailstskgvlt
drearklgvggelicevw

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >3d5cI (I:)
meqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfd
ayitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkar
rapqyskr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cI (I:)
eqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfda
yitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkarr
apqyskr

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >3d5cJ (J:)
mpkiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsr
ehfelrthnrlvdiinpnrktieqlmtldlptgveieiktvgggr

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cJ (J:)
kiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsreh
felrthnrlvdiinpnrktieqlmtldlptgveieikt

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >3d5cK (K:)
makkpskkkvkrqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpya
aqlaaldaakkamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcr
pkkkfrkas

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cK (K:)
krqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpyaaqlaaldaak
kamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcrpkkkfrkas

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >3d5cL (L:)
malptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrlt
sgyevtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskyg
tkkpkeaaktaakk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cL (L:)
ptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrltsgy
evtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskygtkk
pkea

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >3d5cN (N:)
markaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkas
w

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cN (N:)
arkaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkasw

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >3d5cO (O:)
mpitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmv
gqrrrllrylqredperyralieklgirg

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cO (O:)
pitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmvg
qrrrllrylqredperyralieklgirg

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >3d5cP (P:)
mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
svgaqptdtarrllrqagvfrqearega

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cP (P:)
mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
svgaqptdtarrllrqagvfrqe

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >3d5cQ (Q:)
mpkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveii
esrpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cQ (Q:)
pkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveiie
srpiskrkrfrvlrlvesgrmdlvekylirrqnyqslsk

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >3d5cR (R:)
mstknakpkkeaqrrpsrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsa
keqrilaktikrarilgllpfteklvrk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cR (R:)
kakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsakeqrilaktikrarilgl
lpfteklvrk

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >3d5cS (S:)
mprslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpv
yitenmvghklgefaptrtyrghgkeakatkkk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cS (S:)
slkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpvyit
enmvghklgefaptrtyr

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >3d5cT (T:)
maqkkpkrnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkae
slidkaakgstlhknaaarrksrlmrkvrqlleaagapliggglsa

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cT (T:)
rnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkaeslidkaa
kgstlhknaaarrksrlmrkvrqlleaagapliggglsa

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >3d5cU (U:)
mgkgdrrtrrgkiwrgtygkyrprkkk

    Sequence, based on observed residues (ATOM records): (download) 
    >3d5cU (U:)
gkgdrrtrrgkiwrgtygkyrprk

  • Chain 'V':
    No sequence available.

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.