PDB entry 6ugm

View 6ugm on RCSB PDB site
Description: structural basis of compass ecm recognition of an unmodified nucleosome
Deposited on 2019-09-26, released 2019-11-20
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.7 Å
R-factor: N/A
AEROSPACI score: 0.06 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: histone h3
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h3g, H3l
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj, LOC494591, XELAEV_18003602mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: histone h2b
    Species: Xenopus laevis [TaxId:8355]
    Gene: XELAEV_18032686mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: histone h3
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h3g, H3l
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj, LOC494591, XELAEV_18003602mg
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: DNA (146-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: DNA (146-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'K':
    Compound: Swd3
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_E24487g
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Bre2
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_C10945g
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: histone-lysine n-methyltransferase, h3 lysine-4 specific
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: SET1, KLLA0F24134g
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6CIT4 (0-274)
      • conflict (35)
  • Chain 'N':
    Compound: Swd1
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_A08800g
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: Sdc1
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_E03521g
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: Sdc1
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_E03521g
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: H3 N-terminus
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • PDB 6UGM (0-2)
  • Chain 'X':
    Compound: Spp1
    Species: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) [TaxId:284590]
    Gene: KLLA0_D07260g
    Database cross-references and differences (RAF-indexed):
  • Heterogens: SAM, 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:
    >6ugmA (A:)
    artkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
    lirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvglfedtnlcgihakrvtim
    pkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records):
    >6ugmA (A:)
    phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqease
    aylvglfedtnlcgihakrvtimpkdiqlarrirger
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6ugmB (B:)
    sgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkv
    flenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records):
    >6ugmB (B:)
    kvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrk
    tvtamdvvyalkrqgrtlygfg
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6ugmC (C:)
    akaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaar
    dnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6ugmD (D:)
    pepaksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskams
    imnsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtk
    ytsak
    

    Sequence, based on observed residues (ATOM records):
    >6ugmD (D:)
    trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6ugmE (E:)
    artkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
    lirklpfqrlvreiaqdfktdlrfqssavmalqeaseaylvglfedtnlcgihakrvtim
    pkdiqlarrirgera
    

    Sequence, based on observed residues (ATOM records):
    >6ugmE (E:)
    hryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeasea
    ylvglfedtnlcgihakrvtimpkdiqlarrirger
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6ugmF (F:)
    sgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkv
    flenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records):
    >6ugmF (F:)
    rhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteha
    krktvtamdvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >6ugmG (G:)
    akaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaar
    dnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6ugmH (H:)
    pepaksapapkkgskkavtktqkkdgkkrrksrkesyaiyvykvlkqvhpdtgisskams
    imnsfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtk
    ytsak
    

    Sequence, based on observed residues (ATOM records):
    >6ugmH (H:)
    srkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6ugmK (K:)
    mcdldsvsdltltlrmlqfdkqvlpasgkistscqispdgeliaicqntdmlvyeisssk
    mmklttthkecinclcwspdskciasgsedftveithiiygrirrlmghtapvisicynn
    kgnilcsssmdesikewhvlsgtalktmsahsdavvsidipkfdssilssgsydglirif
    dtesghclktltydkdwiaedgvvpistvkfsrngkfllvksldnvvklweytrgtvvrt
    flwphqetkaklkyncgleliypqgkdplvisgndsgsmcvwnvysknlvqkidekhrns
    plisisasydkvatlslngecnlfrvh
    

    Sequence, based on observed residues (ATOM records):
    >6ugmK (K:)
    mlqfdkqvlpasgkistscqispdgeliaicqntdmlvyeissskmmklttthkecincl
    cwspdskciasgsedftveithiiygrirrlmghtapvisicynnkgnilcsssmdesik
    ewhvlsgtalktmsahsdavvsidipkfdssilssgsydglirifdtesghclktltydk
    dwiaedgvvpistvkfsrngkfllvksldnvvklweytrgtvvrtflwpklkyncgleli
    ypqgkdplvisgndsgsmcvwnvysknlvqkidekhrnsplisisasydkvatlslngec
    nlfrv
    

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6ugmL (L:)
    msvpvipyldydivdlgsdikkpdfpqlseshrineqqyyitedtplnkrnfmyqpcaan
    lmldklkycgtdyfdkssinlmdrsdklafslddhsvsvsencgwrsvrsdvcmkegkiy
    wevevknvsdtshircgisrreastetpvgcdfygysirdkglqvihegrlhtvlkphem
    qagdrigflltlpslqsqseqamdyslkriqelnnddsrtnkrnkkfnkefykfllrsce
    ptnvvrdqiairyknqlfyestdyvkttkpeyydnrddmqkfyelenssfevfvngvshg
    iafegltpflppfselqynekfylhhwnkrnvtkgieirnkyvnnnrlgyyatlssfqgg
    tasiiteamelkflpkdvdiktlndiyneqiasdivwdlideidt
    

    Sequence, based on observed residues (ATOM records):
    >6ugmL (L:)
    svpvipyldydivdlgsdikkpdfpqlseshrineqqyyitedtplnkrnfmyqpcaanl
    mldklkycgtdyfdkssinlmdrsdklafslddhsvsvsencgwrsvrsdvcmkegkiyw
    evevknvsdtshircgisrreastetpvgcdfygysirdkglqvihegrlhtvlkphemq
    agdrigflltlpslqsqseqamdyslkriqelnnkfnkefykfllrsceptnvvrdqiai
    ryknqlfyestdyvkttkpeyydnrddmqkfyelenssfevfvngvshgiafegltpflp
    pfselqynekfylhheirnkyvnnnrlgyyatlssfqggtasiiteamelkflpkdvdik
    tlndiyneqiasdivwdlidei
    

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6ugmM (M:)
    yqqieqngiirdnqialnekefdstlasttgsfiaegfkkipdklkssyllhhrrlaqpl
    ntvhnhqeqnfmalngtestnqeadleqdnhnassrlnrvfqrrfqqdieaqraaigfes
    dllslnqltkrkkpvtfarsaihnwglyalepiaakemiieyvgesirqpvaemrekryi
    ksgigssylfridentvidatkrggiarfinhccepsctakiikvdgrkriviyalrdig
    tneeltydykferetdegerlpclcgapsckgfln
    

    Sequence, based on observed residues (ATOM records):
    >6ugmM (M:)
    yqqieqngiirdnqialnekefdstlasttgsfiaegfkkipdklkssnqltkrkkpvtf
    arsaihnwglyalepiaakemiieyvgesirqpvaemrekryiksgigssylfridentv
    idatkrggiarfinhccepsctakiikvdgrkriviyalrdigtneeltydykfpclcga
    psckgfln
    

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6ugmN (N:)
    manlllqdpfgvlkeypeklthtlevpvaavcvkfsprgdylavgcsngaiiiydmdslk
    piamlgthsgahtrsvqsvcwsndgrylwssgrdwyaklwdmtqptkcfqqykfdgplws
    chvvrwnvcivtvveeptayvltltdrqnafhcfplleqdqdisghgytlvacphpties
    iiitgtskgwinafqldlesgfedkirccyeekiananikqiiispsgtriaingsdrti
    rqyqlivedneseggsshsvsielehkyqdiinrlqwntiffsnhsgeylvasahgssah
    dlylwetssgslvrvlegadeelldidwnfysmriasngfesgwvymwsivippkwsala
    pdfeeveenidyqekenefdimdddnnlqamteaeeiaidlctpekydvrgndismpsfv
    ipidyegviiqqhwahqeq
    

    Sequence, based on observed residues (ATOM records):
    >6ugmN (N:)
    anlllqdpfgvlkeypeklthtlevpvaavcvkfsprgdylavgcsngaiiiydmdslkp
    iamlgthsgahtrsvqsvcwsndgrylwssgrdwyaklwdmtqptkcfqqykfdgplwsc
    hvvrwnvcivtvveeptayvltltdrqnafhcfplleqdqdisghgytlvacphptiesi
    iitgtskgwinafqldledkirccyeekiananikqiiispsgtriaingsdrtirqyql
    ivehsvsielehkyqdiinrlqwntiffsnhsgeylvasahgssahdlylwetssgslvr
    vlegadeelldidwnfysmriasngfesgwvymwsivippkwsalapdfeeveenidyqe
    kenefdieeiaidlctpekydvrgndismpsfvipidyegviiqqhwa
    

  • Chain 'O':
    Sequence, based on SEQRES records:
    >6ugmO (O:)
    msepvmenmapedvvklekeehivpdigvssistteplspsgipressgtvtsataatte
    revspkkelqidhdrvdpvamiggsttrrylnehvtkhllegmkliarekpedplrvlgq
    flidasemnqkpss
    

    Sequence, based on observed residues (ATOM records):
    >6ugmO (O:)
    sttrrylnehvtkhllegmkliarekpedplrvlgqflidas
    

  • Chain 'P':
    Sequence, based on SEQRES records:
    >6ugmP (P:)
    msepvmenmapedvvklekeehivpdigvssistteplspsgipressgtvtsataatte
    revspkkelqidhdrvdpvamiggsttrrylnehvtkhllegmkliarekpedplrvlgq
    flidasemnqkpss
    

    Sequence, based on observed residues (ATOM records):
    >6ugmP (P:)
    pvamiggsttrrylnehvtkhllegmklidplrvlgqflidas
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >6ugmR (R:)
    tmq
    

  • Chain 'X':
    Sequence, based on SEQRES records:
    >6ugmX (X:)
    mslpswcprydsrkhdpktgeevycickkpdtgelmvgcdgcddwfhfsclkipekyrdl
    vfsfycsycsagitgpalinggklpktlwkrkcrlpecytecdansrskycskkhavqyv
    qsivdklnlpgvdkiallrqllnettsleefktlgrdklpevtsplskdqyskllendqh
    lnklinehdelvsvklsklneedaviekyvnwigevnerlsphfnqptgrkksksaskvt
    icgyhneftiprsveefldkllqlkedensnitsvdgvcvktkcakhqdwitlsqndlse
    qkdslenvkrrldllisvrtnqlrisffeqemsnrvlpgvkt
    

    Sequence, based on observed residues (ATOM records):
    >6ugmX (X:)
    klsklneedaviekyvnwigevnerlsphfnqptgwitlsqndlseqkdslenvkrrldl
    lisvrtnqlrisf