PDB entry 6v4x

View 6v4x on RCSB PDB site
Description: cryo-em structure of an active human histone pre-mrna 3'-end processing machinery at 3.2 angstrom resolution
Deposited on 2019-12-02, released 2020-02-19
The last revision was dated 2022-03-16, with a file datestamp of 2022-03-11.
Experiment type: EM
Resolution: 3.2 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Small nuclear ribonucleoprotein Sm D3
    Species: Homo sapiens [TaxId:9606]
    Gene: SNRPD3
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62318 (20-145)
      • expression tag (0-19)
  • Chain 'B':
    Compound: small nuclear ribonucleoprotein-associated proteins b and b'
    Species: Homo sapiens [TaxId:9606]
    Gene: SNRPB, COD, SNRPB1
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: U7 snRNA-associated Sm-like protein LSm10
    Species: Homo sapiens [TaxId:9606]
    Gene: LSM10
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: U7 snRNA-associated Sm-like protein LSm11
    Species: Homo sapiens [TaxId:9606]
    Gene: LSM11
    Database cross-references and differences (RAF-indexed):
    • Uniprot P83369 (11-220)
      • expression tag (0-10)
    • Uniprot P83369 (221-258)
  • Chain 'E':
    Compound: Small nuclear ribonucleoprotein E
    Species: Homo sapiens [TaxId:9606]
    Gene: SNRPE
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Small nuclear ribonucleoprotein F
    Species: Homo sapiens [TaxId:9606]
    Gene: SNRPF, PBSCF
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Small nuclear ribonucleoprotein G
    Species: Homo sapiens [TaxId:9606]
    Gene: SNRPG, PBSCG
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62308 (0-75)
      • expression tag (76-83)
  • Chain 'H':
    Compound: Cleavage and polyadenylation specificity factor subunit 3
    Species: Homo sapiens [TaxId:9606]
    Gene: CPSF3, CPSF73
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: Cleavage and polyadenylation specificity factor subunit 2
    Species: Homo sapiens [TaxId:9606]
    Gene: CPSF2, CPSF100, KIAA1367
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: Symplekin
    Species: Homo sapiens [TaxId:9606]
    Gene: SYMPK, SPK
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: modified H2a pre-mRNA
    Species: MUS MUSCULUS, synthetic [TaxId:10090]
  • Chain 'Z':
    Compound: U7 snRNA
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
  • Heterogens: ZN

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 'A':
    Sequence, based on SEQRES records:
    >6v4xA (A:)
mgsshhhhhhssglvprgshmsigvpikvlheaeghivtcetntgevyrgklieaednmn
cqmsnitvtyrdgrvaqleqvyirgskirflilpdmlknapmlksmknknqgsgagrgka
ailkaqvaargrgrgmgrgnifqkrr

    Sequence, based on observed residues (ATOM records):
    >6v4xA (A:)
sigvpikvlheaeghivtcetntgevyrgklieaednmncqmsnitvtyrdgrvaqleqv
yirgskirflilpdmlknapmlk

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6v4xB (B:)
mtvgksskmlqhidyrmrcilqdgrifigtfkafdkhmnlilcdcdefrkikpknskqae
reekrvlglvllrgenlvsmtvegpppkdtgiarv

    Sequence, based on observed residues (ATOM records):
    >6v4xB (B:)
tvgksskmlqhidyrmrcilqdgrifigtfkafdkhmnlilcdcdefrkreekrvlglvl
lrgenlvsmtvegppp

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6v4xC (C:)
mavshsvkertisensliillqglqgrvttvdlrdesvahgridnvdafmnirlakvtyt
drwghqvklddlfvtgrnvryvhipddvnitstieqqlqiihrvrnfggkgqgrwefppk
nck

    Sequence, based on observed residues (ATOM records):
    >6v4xC (C:)
mavshsvkertisensliillqglqgrvttvdlrdesvahgridnvdafmnirlakvtyt
drwghqvklddlfvtgrnvryvhipddvnitstieqqlqiihrvrnfggkgqgr

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6v4xD (D:)
mhhhhhhsggsmeerergarsagagsparppsprldvssdsfdpllalyaprlppipypn
apcfnnvaeyesflrtgvrgggrgrgrargaaagsgvpaapgpsgrtrrrpdapapdper
iqrlrrlmvakeegdgaagagrrgpgrsrkaprnvltrmplhegsplgelhrciregvkv
nvhirtfkglrgvctgflvafdkfwnmaltdvdetyrkpvlqsrkkkrkpkvdyqqvftr
hinqifirgenvllvhlaq

    Sequence, based on observed residues (ATOM records):
    >6v4xD (D:)
periqrlrrlmvkaprnvltrmplhegsplgelhrciregvkvnvhirtfkglrgvctgf
lvafdkfwnmaltdvdetyrkpqqvftrhinqifirgenvllvhla

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6v4xE (E:)
mayrgqgqkvqkvmvqpinlifrylqnrsriqvwlyeqvnmriegciigfdeymnlvldd
aeeihsktksrkqlgrimlkgdnitllqsvsn

    Sequence, based on observed residues (ATOM records):
    >6v4xE (E:)
vqkvmvqpinlifrylqnrsriqvwlyeqvnmriegciigfdeymnlvlddaeeihsktk
srkqlgrimlkgdnitllqsv

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6v4xF (F:)
mslplnpkpflngltgkpvmvklkwgmeykgylvsvdgymnmqlanteeyidgalsghlg
evlircnnvlyirgveeeeedgemre

    Sequence, based on observed residues (ATOM records):
    >6v4xF (F:)
lplnpkpflngltgkpvmvklkwgmeykgylvsvdgymnmqlanteeyidgalsghlgev
lircnnvlyirgve

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6v4xG (G:)
mskahppelkkfmdkklslklnggrhvqgilrgfdpfmnlvidecvematsgqqnnigmv
virgnsiimlealervlehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6v4xG (G:)
ahppelkkfmdkklslklnggrhvqgilrgfdpfmnlvidecvematsgqqnnigmvvir
gnsiimlealervlehh

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6v4xH (H:)
msaipaeesdqllirplgagqevgrsciilefkgrkimldcgihpglegmdalpyidlid
paeidlllishfhldhcgalpwflqktsfkgrtfmthatkaiyrwllsdyvkvsnisadd
mlytetdleesmdkietinfhevkevagikfwcyhaghvlgaamfmieiagvkllytgdf
srqedrhlmaaeipnikpdiliiestygthihekreerearfcntvhdivnrggrglipv
falgraqelllildeywqnhpelhdipiyyasslakkcmavyqtyvnamndkirkqinin
npfvfkhisnlksmdhfddigpsvvmaspgmmqsglsrelfeswctdkrngviiagycve
gtlakhimsepeeittmsgqklplkmsvdyisfsahtdyqqtsefiralkpphvilvhge
qnemarlkaalireyedndevhievhnprnteavtlnfrgeklakvmgfladkkpeqgqr
vsgilvkrnfnyhilspcdlsnytdlamstvkqtqaipytgpfnllcyqlqkltgdveel
eiqekpalkvfknitviqepgmvvlewlanpsndmyadtvttvilevqsnpkirkgavqk
vskklemhvyskrleimlqdifgedcvsvkddsilsvtvdgktanlnletrtveceegse
ddeslremvelaaqrlyealtpvh

    Sequence, based on observed residues (ATOM records):
    >6v4xH (H:)
sdqllirplgagqevgrsciilefkgrkimldcgihpglegmdalpyidlidpaeidlll
ishfhldhcgalpwflqktsfkgrtfmthatkaiyrwllsdyvkvsnisaddmlytetdl
eesmdkietinfhevkevagikfwcyhaghvlgaamfmieiagvkllytgdfsrqedrhl
maaeipnikpdiliiestygthihekreerearfcntvhdivnrggrglipvfalgraqe
lllildeywqnhpelhdipiyyasslakkcmavyqtyvnamndkirkqininnpfvfkhi
snlksmdhfddigpsvvmaspgmmqsglsrelfeswctdkrngviiagycvegtlakhim
sepeeittmsgqklplkmsvdyisfsahtdyqqtsefiralkpphvilvhgeqnemarlk
aalireyedndevhievhnprnteavtlnfrgeklakvmgfladgqrvsgilvkrnfnyh
ilspcdlsnytdlamstvk

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6v4xI (I:)
mtsiiklttlsgvqeesalcyllqvdefrflldcgwdehfsmdiidslrkhvhqidavll
shpdplhlgalpyavgklglncaiyatipvykmgqmfmydlyqsrhntedftlftlddvd
aafdkiqqlkfsqivnlkgkghglsitplpaghmiggtiwkivkdgeeeivyavdfnhkr
eihlngcslemlsrpsllitdsfnatyvqprrkqrdeqlltnvletlrgdgnvliavdta
grvlelaqlldqiwrtkdaglgvyslallnnvsynvvefsksqvewmsdklmrcfedkrn
npfqfrhlslchglsdlarvpspkvvlasqpdlecgfsrdlfiqwcqdpknsiiltyrtt
pgtlarflidnpsekiteielrkrvklegkeleeylekeklkkeaakkleqskeadidss
desdieedidqpsahktkhdlmmkgegsrkgsffkqakksypmfpapeerikwdeygeii
kpedflvpelqateeeksklesgltngdepmdqdlsdvptkcisttesieikarvtyidy
egrsdgdsikkiinqmkprqliivhgppeasqdlaeccrafggkdikvympklhetvdat
sethiyqvrlkdslvsslqfckakdaelawidgvldmrvskvdtgvileegelkddgeds
emqveapsdssviaqqkamkslfgddeketgeeseiiptleplpphevpghqsvfmnepr
lsdfkqvllregiqaefvggvlvcnnqvavrrtetgriglegclcqdfyrirdllyeqya
iv

    Sequence, based on observed residues (ATOM records):
    >6v4xI (I:)
tsiiklttlsgvqeesalcyllqvdefrflldcgwdehfsmdiidslrkhvhqidavlls
hpdplhlgalpyavgklglncaiyatipvykmgqmfmydlyqsrhntedftlftlddvda
afdkiqqlkfsqivnlkgkghglsitplpaghmiggtiwkivkdgeeeivyavdfnhkre
ihlngcslemlsrpsllitdsfnatyvqprrkqrdeqlltnvletlrgdgnvliavdtag
rvlelaqlldqiwrtkdaglgvyslallnnvsynvvefsksqvewmsdklmrcfedkrnn
pfqfrhlslchglsdlarvpspkvvlasqpdlecgfsrdlfiqwcqdpknsiiltyrttp
gtlarflidnpsekiteielrkrvkptkcisttesieikarvtyidyegrsdgdsikkii
nqmkprqliivhgppeasqdlaeccrafggkdikvympklhetvdatsethiyqvrlkds
lvsslqfckakdaelawidgvldmiptlep

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6v4xJ (J:)
mttservvdllnqaalitndskitvlkqvqeliinkdptlldnfldeiiafqadksievr
kfvigfieeackrdielllklianlnmllrdenvnvvkkailtmtqlykvalqwmvksrv
iselqeacwdmvsamagdiillldsdndgirthaikfveglivtlsprmadseiprrqeh
disldriprdhpyiqynvlweegkaaleqllkfmvhpaissinlttalgslaniarqrpm
fmseviqayetlhanlpptlaksqvssvrknlklhllsvlkhpaslefqaqittllvdlg
tpqaeiarnmpsskdtrkrprddsdstlkkmklepnlgeddedkdlepgpsgtskasaqi
sgqsdtditaeflqplltpdnvanlvlismvylpeampasfqaiytpvesagteaqikhl
arlmatqmtaaglgpgveqtkqckeepkeekvvktesvlikrrlsaqgqaisvvgslssm
spleeeapqakrrpepiipvtqprlagaggrkkifrlsdvlkpltdaqveamklgavkri
lraekavacsgaaqvrikilaslvtqfnsglkaevlsfiledvrarldlafawlyqeyna
ylaagasgsldkyedclirllsglqekpdqkdgiftkvvleaplitesalevvrkycede
srtylgmstlrdlifkrpsrqfqylhvlldlsshekdkvrsqallfikrmyekeqlreyv
ekfalnylqllvhpnppsvlfgadkdtevaapwteetvkqclylylallpqnhklihela
avyteaiadikrtvlrvieqpirgmgmnspellllvencpkgaetlvtrclhsltdkvpp
spelvkrvrdlyhkrlpdvrflipvlnglekkeviqalpkliklnpivvkevfnrllgtq
hgegnsalsplnpgellialhnidsvkcdmksiikatnlcfaernvytsevlavvmqqlm
eqsplpmllmrtviqsltmyprlggfvmnilsrlimkqvwkypkvwegfikccqrtkpqs
fqvilqlppqqlgavfdkcpelrepllahvrsftphqqahipnsimtileas

    Sequence, based on observed residues (ATOM records):
    >6v4xJ (J:)
mttservvdllnqaalitndskitvlkqvqeliinkdptlldnfldeiiafqadksievr
kfvigfieeackrdielllklianlnmllrdenvnvvkkailtmtqlykvalqwmvksrv
iselqeacwdmvsamagdiillldsdndgirthaikfveglivtlsprmadseiprrqeh
disldriprdhpyiqynvlweegkaaleqllkfmvhpaissinlttalgslaniarqrpm
fmseviqayetlhanlpptlaksqvssvrknlklhllsvlkhpaslefqaqittllvdlg
tpqaeiarnmp

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.