9R8V | pdb_00009r8v

Cryo-EM structure of the human pre-Bact-OTS complex (whole map)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

cryo-EM structure of the human pre-Bact-OTS complex

Zhang, Z., Kumar, V., Dybkov, O., Zhong, J., Kastner, B., Henning, U., Luehrmann, R.

To be published.

Macromolecule Content 

  • Total Structure Weight: 3,268.15 kDa 
  • Atom Count: 80,644 
  • Modeled Residue Count: 14,985 
  • Deposited Residue Count: 27,235 
  • Unique protein chains: 50
  • Unique nucleic acid chains: 4

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 82,769Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O75643 (Homo sapiens)
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GTEx:  ENSG00000144028 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1E [auth 7]793Homo sapiensMutation(s): 0 
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Find proteins for Q15459 (Homo sapiens)
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GTEx:  ENSG00000099995 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinG [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentH [auth C]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinI [auth E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1J [auth G]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AK [auth I]312Homo sapiensMutation(s): 0 
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Find proteins for Q8NAV1 (Homo sapiens)
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GTEx:  ENSG00000134748 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BUD31 homologL [auth Q]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologM [auth R]229Homo sapiensMutation(s): 0 
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Find proteins for Q9P013 (Homo sapiens)
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GTEx:  ENSG00000150316 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
WW domain-binding protein 11N [auth X]641Homo sapiensMutation(s): 0 
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Find proteins for Q9Y2W2 (Homo sapiens)
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GTEx:  ENSG00000084463 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 5O [auth q]73Homo sapiensMutation(s): 0 
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Find proteins for Q9BZL1 (Homo sapiens)
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GTEx:  ENSG00000198258 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2P [auth r]199Homo sapiensMutation(s): 0 
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Find proteins for Q96NC0 (Homo sapiens)
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GTEx:  ENSG00000146007 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2Q [auth 22],
TA [auth 52]		118Homo sapiensMutation(s): 0 
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Find proteins for P62316 (Homo sapiens)
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GTEx:  ENSG00000125743 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''R [auth 2B]225Homo sapiensMutation(s): 0 
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Find proteins for P08579 (Homo sapiens)
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GTEx:  ENSG00000125870 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FS [auth 2f],
WA [auth 5f]		86Homo sapiensMutation(s): 0 
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Find proteins for P62306 (Homo sapiens)
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GTEx:  ENSG00000139343 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'RA [auth 5b],
T [auth 2b]		240Homo sapiensMutation(s): 0 
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Find proteins for P14678 (Homo sapiens)
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GTEx:  ENSG00000125835 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3U [auth 23],
UA [auth 53]		126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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GTEx:  ENSG00000100028 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GV [auth 2g],
XA [auth 5g]		76Homo sapiensMutation(s): 0 
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Find proteins for P62308 (Homo sapiens)
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GTEx:  ENSG00000143977 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EVA [auth 5e],
W [auth 2e]		92Homo sapiensMutation(s): 0 
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Find proteins for P62304 (Homo sapiens)
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GTEx:  ENSG00000182004 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1SA [auth 51],
X [auth 21]		119Homo sapiensMutation(s): 0 
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Find proteins for P62314 (Homo sapiens)
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GTEx:  ENSG00000167088 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'Y [auth 2A]255Homo sapiensMutation(s): 0 
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Find proteins for P09661 (Homo sapiens)
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GTEx:  ENSG00000131876 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4Z [auth B4]424Homo sapiensMutation(s): 0 
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Find proteins for Q15427 (Homo sapiens)
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GTEx:  ENSG00000143368 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3AA [auth 9]501Homo sapiensMutation(s): 0 
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Find proteins for Q12874 (Homo sapiens)
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GTEx:  ENSG00000183431 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2BA [auth 8]464Homo sapiensMutation(s): 0 
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Find proteins for Q15428 (Homo sapiens)
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GTEx:  ENSG00000104897 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2CA [auth B2]895Homo sapiensMutation(s): 0 
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Find proteins for Q13435 (Homo sapiens)
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GTEx:  ENSG00000087365 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5DA [auth B5]86Homo sapiensMutation(s): 0 
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Find proteins for Q9BWJ5 (Homo sapiens)
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GTEx:  ENSG00000169976 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3EA [auth B3]1,217Homo sapiensMutation(s): 0 
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Find proteins for Q15393 (Homo sapiens)
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GTEx:  ENSG00000189091 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1FA [auth B1]1,304Homo sapiensMutation(s): 0 
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Find proteins for O75533 (Homo sapiens)
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GTEx:  ENSG00000115524 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6GA [auth B6]125Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3B4 (Homo sapiens)
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GTEx:  ENSG00000115128 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-catenin-like protein 1HA [auth BL]563Homo sapiensMutation(s): 0 
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Find proteins for Q8WYA6 (Homo sapiens)
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GTEx:  ENSG00000132792 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
U2 snRNP-associated SURP motif-containing proteinIA [auth SR]1,029Homo sapiensMutation(s): 0 
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Find proteins for O15042 (Homo sapiens)
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GTEx:  ENSG00000163714 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX15JA [auth DH]795Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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Find proteins for O43143 (Homo sapiens)
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GTEx:  ENSG00000109606 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein RedLA [auth x],
MA [auth y]		557Homo sapiensMutation(s): 0 
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Find proteins for Q13123 (Homo sapiens)
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GTEx:  ENSG00000113141 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
WD40 repeat-containing protein SMU1NA [auth v],
OA [auth w]		513Homo sapiensMutation(s): 0 
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Find proteins for Q2TAY7 (Homo sapiens)
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GTEx:  ENSG00000122692 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22PA [auth P]500Homo sapiensMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2QA [auth t]520Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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Find proteins for Q13356 (Homo sapiens)
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GTEx:  ENSG00000100023 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2YA [auth 62]95Homo sapiensMutation(s): 0 
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Find proteins for Q9Y333 (Homo sapiens)
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GTEx:  ENSG00000204392 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3ZA [auth 63]102Homo sapiensMutation(s): 0 
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Find proteins for P62310 (Homo sapiens)
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GTEx:  ENSG00000170860 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4AB [auth 64]139Homo sapiensMutation(s): 0 
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Find proteins for Q9Y4Z0 (Homo sapiens)
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GTEx:  ENSG00000130520 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5BB [auth 65]91Homo sapiensMutation(s): 0 
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Find proteins for Q9Y4Y9 (Homo sapiens)
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GTEx:  ENSG00000106355 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6CB [auth 66]80Homo sapiensMutation(s): 0 
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Find proteins for P62312 (Homo sapiens)
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PHAROS:  P62312
GTEx:  ENSG00000164167 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7DB [auth 67]103Homo sapiensMutation(s): 0 
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Find proteins for Q9UK45 (Homo sapiens)
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GTEx:  ENSG00000130332 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8EB [auth 68]96Homo sapiensMutation(s): 0 
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PHAROS:  O95777
GTEx:  ENSG00000128534 
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UniProt GroupO95777
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1FB [auth S1]536Homo sapiensMutation(s): 0 
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Find proteins for Q13573 (Homo sapiens)
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GTEx:  ENSG00000100603 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/arginine-rich splicing factor 1GB [auth A6]248Homo sapiensMutation(s): 0 
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Find proteins for Q07955 (Homo sapiens)
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GTEx:  ENSG00000136450 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription elongation regulator 1HB [auth T]1,098Homo sapiensMutation(s): 0 
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Find proteins for O14776 (Homo sapiens)
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GTEx:  ENSG00000113649 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1IB [auth K]439Homo sapiensMutation(s): 0 
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Find proteins for P55081 (Homo sapiens)
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GTEx:  ENSG00000140259 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17JB [auth P7]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AKB [auth 5A]110Homo sapiensMutation(s): 0 
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Find proteins for Q7RTV0 (Homo sapiens)
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GTEx:  ENSG00000100410 
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Entity ID: 3
MoleculeChains LengthOrganismImage
U2 snRNAC [auth 2]188Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
U6 snRNAD [auth 6]106Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
U5 snRNAF [auth 5]117Homo sapiens
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Entity ID: 37
MoleculeChains LengthOrganismImage
pre-mRNAKA [auth Z]410Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release