PDB entry 6swd

View 6swd on RCSB PDB site
Description: ic2 body model of cryo-em structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi
Deposited on 2019-09-20, released 2020-02-19
The last revision was dated 2020-02-19, with a file datestamp of 2020-02-14.
Experiment type: EM
Resolution: 3.2 Å
R-factor: N/A
AEROSPACI score: 0.1 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 30S ribosomal protein aL41
    Species: PYROCOCCUS ABYSSI GE5 [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6SWD (0-35)
  • Chain '2':
    Compound: 16S ribosomal RNA
    Species: PYROCOCCUS ABYSSI GE5 [TaxId:272844]
  • Chain '5':
    Compound: mRNA
    Species: Pyrococcus abyssi GE5, synthetic [TaxId:272844]
  • Chain '6':
    Compound: translation initiation factor 1a
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Gene: eIF1A, aif1A, PYRAB05910, PAB2441
    Database cross-references and differences (RAF-indexed):
  • Chain 'A':
    Compound: 30S ribosomal protein S3Ae
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 30S ribosomal protein S2
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Zn-ribbon RNA-binding protein involved in translation
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: 30S ribosomal protein S4e
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 30S ribosomal protein S5
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 30S ribosomal protein S6e
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: 30S ribosomal protein S8
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: 30S ribosomal protein S8e
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: 30S ribosomal protein S11
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 30S ribosomal protein S12
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Q':
    Compound: 30S ribosomal protein S15
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: 30S ribosomal protein S17
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'V':
    Compound: 30S ribosomal protein S24e
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Chain 'W':
    Compound: 30s ribosomal protein s27e
    Species: Pyrococcus abyssi (strain GE5 / Orsay) [TaxId:272844]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: LHH, MG, ZN, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain '0':
    Sequence; same for both SEQRES and ATOM records:
    >6swd0 (0:)
mkrrprkwkkkgrmrwkwikkrirrlkrqrkkergl

  • Chain '2':
    No sequence available.

  • Chain '5':
    No sequence available.

  • Chain '6':
    Sequence, based on SEQRES records:
    >6swd6 (6:)
mpkkerkvegdevirvplpegnqlfgvveqalgagwmdvrcedgkirrcripgklrrrvw
irvgdlvivqpwpvqsdkrgdivyrytqtqvdwllrkgkitqefltggsllve

    Sequence, based on observed residues (ATOM records):
    >6swd6 (6:)
virvplpegnqlfgvveqalgagwmdvrcedgkirrcripgklrrrvwirvgdlvivqpw
pvqsdkrgdivyrytqtqvdwllrkgkitqefltg

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6swdA (A:)
maakrrvsaakdkwklkqwyviyapdffggvevgltpaddpekvlnrvvevtlkditgdf
lkghvklyfqvydvkgqnaytkfkgmklarsyirslvrrrttridgifnittkdgyklrv
mamviaarriqtsqerairkimqeiiykkaeelnfkdfvleavngkiaaeiakeakkiyp
lkkaeirkikvlgepevaa

    Sequence, based on observed residues (ATOM records):
    >6swdA (A:)
kdkwklkqwyviyapdffggvevgltpaddpekvlnrvvevtlkditgdflkghvklyfq
vydvkgqnaytkfkgmklarsyirslvrrrttridgifnittkdgyklrvmamviaarri
qtsqerairkimqeiiykkaeelnfkdfvleavngkiaaeiakeakkiyplkkaeirkik
vlgepeva

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6swdB (B:)
madeylvpldqylaagvhigtqqktkdmkkfiyrvrqdglyvldvrktderlkvagkfla
rfdpqsilavsvrlygqkpvkkfgevtgaraipgrflpgtmtnpavknffepdviiitdp
radhqamkeaieigipivalvdtenllsyvdlaiptnnkgrkalaliywilareilynrg
eissreefkipveefemkivrr

    Sequence, based on observed residues (ATOM records):
    >6swdB (B:)
eylvpldqylaagvhigtqqktkdmkkfiyrvrqdglyvldvrktderlkvagkflarfd
pqsilavsvrlygqkpvkkfgevtgaraipgrflpgtmtnpavknffepdviiitdprad
hqamkeaieigipivalvdtenllsyvdlaiptnnkgrkalaliywilareilynrgeis
sreefkipveefemki

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6swdC (C:)
maenvelkfeipvctscgreitprehathfvcpncgeaiiwrcetcrllakpykcpkcgw
egp

    Sequence, based on observed residues (ATOM records):
    >6swdC (C:)
envelkfeipvctscgreitprehathfvcpncgeaiiwrcetcrllakpykcpkcgweg
p

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6swdD (D:)
mgdpkrqrkkyetpphpwikerldrervlmdkyelknkkelwkhetqlknfrrrarrlla
argkqaeiereqllarlkrlgllpedavlddvlsltiedilerrlqtivykkglartmrq
arqlivhghievngqiirspsylvlkeeedtityartspfanpqhpermmiekakqggea

    Sequence, based on observed residues (ATOM records):
    >6swdD (D:)
gdpkrqrkkyetpphpwikerldrervlmdkyelknkkelwkhetqlknfrrrarrllaa
rgkqaeiereqllarlkrlgllpedavlddvlsltiedilerrlqtivykkglartmrqa
rqlivhghievngqiirspsylvlkeeedtityartspfanpqhpermmiekakq

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6swdE (E:)
markgpkrhlkrlaaptswyierkaykwavrprpgphnmrtsipllyivrdylgyaktar
earkilnegkflvdgrvrkdykfpvgimdvvsipetgehyrvlpnrigklilhpiseeea
nikplrirnkrmvkgakiqlnfhdgtnhliplsekdnyftsytvlmkvpereilevlpfe
kgayvfvtqgknvarkgriveikkfpmgwpdvvtiedeegelfdtlkeyafvvgrdkpri
slp

    Sequence, based on observed residues (ATOM records):
    >6swdE (E:)
arkgpkrhlkrlaaptswyierkaykwavrprpgphnmrtsipllyivrdylgyaktare
arkilnegkflvdgrvrkdykfpvgimdvvsipetgehyrvlpnrigklilhpiseeean
ikplrirnkrmvkgakiqlnfhdgtnhliplsekdnyftsytvlmkvpereilevlpfek
gayvfvtqgknvarkgriveikkfpmgwpdvvtiedeegelfdtlkeyafvvgrdkpris
lp

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6swdF (F:)
msqewkeyakrvldewqpktklgmlvkegqitdiheifrkgyqikepeiidvllpevnar
enqeildialtvrmtdsgrrvrfrvlaavgnrdgyvglgighgrevgiairkainyakln
iieikrgcgswecrcrrphsvpftvegkegsvrvklipgprglglvigdvgkkilrlagi
qdvwsqtlgetrttvnfakavfnalyntnkvvvtpemierygivvgrampasftle

    Sequence, based on observed residues (ATOM records):
    >6swdF (F:)
sqewkeyakrvldewqpktklgmlvkegqitdiheifrkgyqikepeiidvllpevnare
nqeildialtvrmtdsgrrvrfrvlaavgnrdgyvglgighgrevgiairkainyaklni
ieikrgcgswecrcrrphsvpftvegkegsvrvklipgprglglvigdvgkkilrlagiq
dvwsqtlgetrttvnfakavfnalyntnkvvvtpemierygivvgramp

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6swdG (G:)
matfklvisdpktgiakqieitgpeaekligkrigdqipvkelginlnelfgkefpedvk
meirggtdkdgfpmrpdihgprrvrillskgpgfrpkekgerrkktvrgntispeivqvn
vklvy

    Sequence, based on observed residues (ATOM records):
    >6swdG (G:)
atfklvisdpktgiakqieitgpeaekligkrigdqipvkelginlnelfgkefpedvkm
eirggtdkdgfpmrpdihgprrvrillskgpgfrpkekgerrkktvrgntispeivqvnv
klvy

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6swdI (I:)
mtlldplanalshitnservgkrevyikpaskligevlrvmqkygyigefefiddgragv
yrvqllgkinkagaikprfpvkardyerwekrflpafefgilivstsqgvmshkearekg
iggrliayvy

    Sequence, based on observed residues (ATOM records):
    >6swdI (I:)
tlldplanalshitnservgkrevyikpaskligevlrvmqkygyigefefiddgragvy
rvqllgkinkagaikprfpvkardyerwekrflpafefgilivstsqgvmshkearekgi
ggrliayvy

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6swdJ (J:)
maiwqgrslrkpsggrivlarkkrkrelgrepsntrvaeqdkrkiirtyggnkkvrltaa
ayanvfdksgkgrkvriirvienpanrqfarrniitkgaiieteigkakvtsrpgqdgvv
naillee

    Sequence, based on observed residues (ATOM records):
    >6swdJ (J:)
aiwqgrslrkpsggrivlarkkrkrelgrepsntrvaeqdkrkiirtyggnkkvrltaaa
yanvfdksgkgrkvriirvienpanrqfarrniitkgaiieteigkakvtsrpgqdgvvn
aillee

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6swdM (M:)
mseeqvnikkkekwgiahiyssynntiihitditgaetisrwsggmvvkadrdepspyaa
mlaarraaeealekgivgvhirvrapggsksktpgpgaqaairalaraglkigrvedvtp
iphdgtrpkggrrgrrv

    Sequence, based on observed residues (ATOM records):
    >6swdM (M:)
kkekwgiahiyssynntiihitditgaetisrwsggmvvkadrdepspyaamlaarraae
ealekgivgvhirvrapggsksktpgpgaqaairalaraglkigrvedvtpiphdgtrpk
ggrrgrrv

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6swdN (N:)
mpgkkapngefagrklklkrkkfrwsdirykrrvlrlkeksdplegapqargivlekiav
eakqpnsgmrkavrvqlikngkvvtafcpgdgaikfidehdeviiegiggpkggsmgdip
girykvvkvnrvslkelvkgrkekprr

    Sequence, based on observed residues (ATOM records):
    >6swdN (N:)
pgkkapngefagrklklkrkkfrwsdirykrrvlrlkeksdplegapqargivlekiave
akqpnsgmrkavrvqlikngkvvtafcpgdgaikfidehdeviiegiggpkggsmgdipg
irykvvkvnrvslkelvkgrkekprr

  • Chain 'Q':
    Sequence, based on SEQRES records:
    >6swdQ (Q:)
marmharkrgksgskrpprtappiwleytvedienlvvklrkegystamigtilrdqygi
ptvklfrdpdnpnrkltitrilekhglapeipedlmflikravnlrkhleqhpkdlhsmr
glqlieskirrlvkyykrkgklpkdwrydpeqakllvr

    Sequence, based on observed residues (ATOM records):
    >6swdQ (Q:)
armharkrgksgskrpprtappiwleytvedienlvvklrkegystamigtilrdqygip
tvklfrdpdnpnrkltitrilekhglapeipedlmflikravnlrkhleqhpkdlhsmrg
lqlieskirrlvkyykrkgklpkdwrydpeqa

  • Chain 'R':
    Sequence, based on SEQRES records:
    >6swdR (R:)
mvrdiglriqppaekcddpkcpwhghlkihgrvfegivvsdkprktvtverqyyhylkky
eryelrrsrihahnppcinakvgdrvliaetrplsktkhfvvvavleraeerr

    Sequence, based on observed residues (ATOM records):
    >6swdR (R:)
vrdiglriqppaekcddpkcpwhghlkihgrvfegivvsdkprktvtverqyyhylkkye
ryelrrsrihahnppcinakvgdrvliaetrplsktkhfvvvavlerae

  • Chain 'V':
    Sequence, based on SEQRES records:
    >6swdV (V:)
meikitevkenkligrkeiyfeiyhpgeptpsrkdvkgklvamldlnpettviqyirsyf
gsykskgyakyyydkdrmlyiepeyilirdgiiekkege

    Sequence, based on observed residues (ATOM records):
    >6swdV (V:)
meikitevkenkligrkeiyfeiyhpgeptpsrkdvkgklvamldlnpettviqyirsyf
gsykskgyakyyydkdrmlyiepeyilirdgiie

  • Chain 'W':
    Sequence, based on SEQRES records:
    >6swdW (W:)
malprnvipmprsrflrvkcidcgneqivfshpatrvrcnvcgatlveptggkgiiraki
levle

    Sequence, based on observed residues (ATOM records):
    >6swdW (W:)
alprnvipmprsrflrvkcidcgneqivfshpatrvrcnvcgatlveptggkgiirakil
evl