PDB entry 6ven

View 6ven on RCSB PDB site
Description: yeast compass in complex with a ubiquitinated nucleosome
Deposited on 2020-01-02, released 2020-01-15
The last revision was dated 2020-01-22, with a file datestamp of 2020-01-17.
Experiment type: EM
Resolution: 3.37 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233 (0-134)
      • engineered mutation (3)
      • engineered mutation (89)
      • engineered mutation (101)
      • engineered mutation (119)
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Histone H2A type 1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06897
      • engineered mutation (98)
  • Chain 'D':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281
      • engineered mutation (28)
      • engineered mutation (116)
  • Chain 'E':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233
      • engineered mutation (89)
      • engineered mutation (101)
      • engineered mutation (119)
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Histone H2A type 1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06897
      • engineered mutation (98)
  • Chain 'H':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281
      • engineered mutation (28)
      • engineered mutation (116)
  • Chain 'I':
    Compound: 601 DNA (146-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: 601 DNA (146-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'K':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: COMPASS component SWD3
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SWD3, CPS30, SAF35, YBR175W, YBR1237
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: COMPASS component SWD1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SWD1, CPS50, SAF49, YAR003W, FUN16
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: histone-lysine n-methyltransferase, h3 lysine-4 specific
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SET1, KMT2, YTX1, YHR119W
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: COMPASS component BRE2
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: BRE2, CPS60, YLR015W
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: COMPASS component SDC1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SDC1, CPS25, SAF19, YDR469W
    Database cross-references and differences (RAF-indexed):
  • Chain 'Q':
    Compound: COMPASS component SDC1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SDC1, CPS25, SAF19, YDR469W
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: COMPASS component SPP1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: SPP1, CPS40, SAF41, YPL138C
    Database cross-references and differences (RAF-indexed):
  • Heterogens: ZN, SAM

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:
    >6venA (A:)
artlqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
lirklpfqrlvreiaqdfktdlrfqssavlalqeaseaylvalfedtnlcaihakrvtil
pkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6venA (A:)
artlqtarphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssav
lalqeaseaylvalfedtnlcaihakrvtilpkdiqlarrirgera

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

    Sequence, based on observed residues (ATOM records):
    >6venB (B:)
lrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktv
tamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6venC (C:)
sgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylta
eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
essksaksk

    Sequence, based on observed residues (ATOM records):
    >6venC (C:)
ktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaardnk
ktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllp

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6venD (D:)
aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyts
ak

    Sequence, based on observed residues (ATOM records):
    >6venD (D:)
ktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstit
sreiqtavrlllpgelakhavsegtkavtcyts

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6venE (E:)
artlqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkstel
lirklpfqrlvreiaqdfktdlrfqssavlalqeaseaylvalfedtnlcaihakrvtil
pkdiqlarrirgera

    Sequence, based on observed residues (ATOM records):
    >6venE (E:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavlalqease
aylvalfedtnlcaihakrvtilpkdiqlarrirger

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

    Sequence, based on observed residues (ATOM records):
    >6venF (F:)
vlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrkt
vtamdvvyalkrqgrtlygf

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6venG (G:)
sgrgkqggktrakaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleylta
eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
essksaksk

    Sequence, based on observed residues (ATOM records):
    >6venG (G:)
kaktrssraglqfpvgrvhrllrkgnyaervgagapvylaavleyltaeilelagnaard
nkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6venH (H:)
aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtcyts
ak

    Sequence, based on observed residues (ATOM records):
    >6venH (H:)
ktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstit
sreiqtavrlllpgelakhavsegtkavtcytsa

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6venK (K:)
gshmmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtl
sdyniqkestlhlvlrlrgc

    Sequence, based on observed residues (ATOM records):
    >6venK (K:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrg

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6venL (L:)
mfqfvtpvgtqnglkatcakispdgqflaitqglniliydinrrtvsqtlvtsharpfse
lcwspdgqciatasddfsveiihlsygllhtfightapvisltfnrkgnllftssmdesi
kiwdtlngslmktisahseavvsvdvpmndssilssgsydglirifdaetghclktltyd
kdwkrengvvpisqvkfsenaryllvksldgvvkiwdciggcvvrtfqvqplekgvlhhs
cgmdflnpedgstplvisgyengdiycwnsdtksllqlldgslyhhsspvmsihcfgnim
cslalngdcclwrwv

    Sequence, based on observed residues (ATOM records):
    >6venL (L:)
mfqfvtpvgtqnglkatcakispdgqflaitqglniliydirtvsqtlvtsharpfselc
wspdgqciatasddfsveiihlsygllhtfightapvisltfnrkgnllftssmdesiki
wdtlngslmktisahseavvsvdvpmndssilssgsydglirifdaetghclktltydkd
wkrengvvpisqvkfsenaryllvksldgvvkiwdciggcvvrtfqvqplekgvlhhscg
mdflnpedgstplvisgyengdiycwnsdtksllqlldgshsspvmsihcfgnimcslal
ngdcclwr

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6venM (M:)
mnillqdpfavlkehpeklthtienplrteclqfspcgdylalgcangalviydmdtfrp
icvpgnmlgahvrpitsiawspdgrllltssrdwsiklwdlskpskplkeirfdspiwgc
qwldakrrlcvatifeesdayvidfsndpvasllsksdekqlsstpdhgyvlvctvhtkh
pniiivgtskgwldfykfhslyqtecihslkitssnikhlivsqngerlaincsdrtirq
yeisiddensaveltlehkyqdvinklqwncilfsnntaeylvasthgssahelyiwett
sgtlvrvlegaeeelidinwdfysmsivsngfesgnvyvwsvvippkwsalapdfeevee
nvdylekedefdevdeaeqqqgleqeeeiaidlrtreqydvrgnnllverftiptdytri
ikmqss

    Sequence, based on observed residues (ATOM records):
    >6venM (M:)
mnillqdpfavlkehpeklthtienplrteclqfspcgdylalgcangalviydmdtfrp
icvpgnmlgahvrpitsiawspdgrllltssrdwsiklwdlskpskplkeirfdspiwgc
qwldrrlcvatifeesdayvidfsndpvaslhgyvlvctvhtkhpniiivgtskgwldfy
kfhslyqtecihslkitssnikhlivsqngerlaincsdrtirqyeisiddensaveltl
ehkyqdvinklqwncilfsnntaeylvasthgssahelyiwettsgtlvrvlegaeeeli
dinwdfysmsivsngfesgnvyvwsvvippkwsalapdfeeveenvdylekedefdevee
eiaidlrtreqydvrgnnllverftiptdytriik

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6venN (N:)
mhhhhhhgssdykdhdgdykdhdidykddddkenlyfqgmdlqnaikdeedmlilkqlls
tytptvtpetsaaleykiwqsrrkvleeekasdwqielngtlfdselqpgssfkaegfrk
iadklkinylphrrrvhqplntvnihnerneytpelcqreessnkepsdsvpqevsssrd
nrasnrrfqqdieaqkaaigtesellslnqlnkrkkpvmfarsaihnwglyaldsiaake
miieyvgerirqpvaemrekrylkngigssylfrvdentvidatkkggiarfinhccdpn
ctakiikvggrrriviyalrdiaaseeltydykferekddeerlpclcgapnckgfln

    Sequence, based on observed residues (ATOM records):
    >6venN (N:)
srrkvleeekasdwqielngtlfdselqpgssfkaegfrkiadklkinvsssrdnrasnr
rfqqdieaqkaaillslnqlnkrkkpvmfarsaihnwglyaldsiaakemiieyvgerir
qpvaemrekrylkngigssylfrvdentvidatkkggiarfinhccdpnctakiikvggr
rriviyalrdiaaseeltydykfepclcgapnckgfln

  • Chain 'O':
    Sequence, based on SEQRES records:
    >6venO (O:)
mklgiipyqegtdivyknalqgqqegkrpnlpqmeathqikssvqgtsyefvrtedipln
rrhfvyrpcsanpfftilgygcteypfdhsgmsvmdrseglsisrdgndlvsvpdqygwr
tarsdvcikegmtywevevirggnkkfadgvnnkenaddsvdevqsgiyekmhkqvndtp
hlrfgvcrreasleapvgfdvygygirdislesihegklncvlengsplkegdkigflls
lpsihtqikqakeftkrrifalnshmdtmnepwredaengpsrkklkqettnkefqrall
edieyndvvrdqiairyknqlffeatdyvkttkpeyyssdkrerqdyyqledsylaifqn
gkylgkafenlkpllppfselqynekfylgywqhgeardesndknttsakkkkqqqkkkk
glilrnkyvnnnklgyyptiscfnggtariiseedkleyldqirsaycvdgnskvntldt
lykeqiaedivwdiideleqialqq

    Sequence, based on observed residues (ATOM records):
    >6venO (O:)
fvrtediplnrrhfvyrpcsanpfftilgygcteypfdhsgmsvmdrseglsidlvsvpd
qygwrtarsdvcikegmtywevevtphlrfgvcrreasleapvgfdvygygirdislesi
hegklncvlengsplkegdkigfllslpsihtqikqakeftkrrifalnsnkefqraley
ndvvrdqiairyknqlffeatdyvkttkpeydyyqledsylaifqngkylgkafenlkpl
lfselqynekfylgywnnnklgyyptiscfnggtariiseedkleyldqirvntldtlyk
eqiaedivwdiidel

  • Chain 'P':
    Sequence, based on SEQRES records:
    >6venP (P:)
mnesenspqhnevtvpmvedtssnadipmeqiqrednknydkhdnecfdmngnhnnnsdn
lqfdsvpssatkdlkniksvtnqnvkieessstnsvieessepkisklenvnlaatvggs
qtrkylntnvtphllagmrliavqqpedplrvlgeylieqsnilksgekesnask

    Sequence, based on observed residues (ATOM records):
    >6venP (P:)
sqtrkylntnvtphllagmrliavqqpedplrvlgeylieqs

  • Chain 'Q':
    Sequence, based on SEQRES records:
    >6venQ (Q:)
mnesenspqhnevtvpmvedtssnadipmeqiqrednknydkhdnecfdmngnhnnnsdn
lqfdsvpssatkdlkniksvtnqnvkieessstnsvieessepkisklenvnlaatvggs
qtrkylntnvtphllagmrliavqqpedplrvlgeylieqsnilksgekesnask

    Sequence, based on observed residues (ATOM records):
    >6venQ (Q:)
ntnvtphllagmrlidplrvlgeylieqs

  • Chain 'R':
    Sequence, based on SEQRES records:
    >6venR (R:)
mwshpqfekgggsgggsggssawshpqfekgsenlyfqgslpqwcpphstlkrnpttged
vycickrpdygelmvgcdgcddwfhftclhipeqfkdlvfsfycpycqagitgknkdaii
ngegslpktlwkrkcrisdcykpclqdskycseehgrefvndiwsrlktdedravvkkmv
eqtghidkfkkfgqldfidnnivvktddekeifdqivvrdmtlktleddlqevqeislpl
fkkklellevylgwldnvytemrkldddaashvecgkedskgtkrkkkknssrsrarkni
cgycstyeripcsveefvrdfgsneeatkihevctkwkcnrhldwvstnqeqylqqidsl
esmqerlqhliqarkkqlniqyyeeilrrgl

    Sequence, based on observed residues (ATOM records):
    >6venR (R:)
lfkkklellevylgwldnvytemrkldddaashvecgkednicgycstyeripcsveefv
rdfgsneeatkihevctkwkcnrhldwvstnqeqylqqidslesmqerlqhliqarkkql
niqyyeeil