6KIU

Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of nucleosome recognition and modification by MLL methyltransferases

Xue, H.Yao, T.Cao, M.Zhu, G.Li, Y.Yuan, G.Chen, Y.Lei, M.Huang, J.

(2019) Nature --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
135Xenopus laevisMutation(s): 0 
Find proteins for A0A310TTQ1 (Xenopus laevis)
Go to UniProtKB:  A0A310TTQ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj (LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase 2A
K
216Homo sapiensMutation(s): 0 
Gene Names: KMT2A (ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1)
EC: 2.1.1.43
Find proteins for Q03164 (Homo sapiens)
Go to Gene View: KMT2A
Go to UniProtKB:  Q03164
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-binding protein 5
N
538Homo sapiensMutation(s): 0 
Gene Names: RBBP5 (RBQ3)
Find proteins for Q15291 (Homo sapiens)
Go to Gene View: RBBP5
Go to UniProtKB:  Q15291
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
R
334Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Set1/Ash2 histone methyltransferase complex subunit ASH2
T
534Homo sapiensMutation(s): 0 
Gene Names: ASH2L (ASH2L1)
Find proteins for Q9UBL3 (Homo sapiens)
Go to Gene View: ASH2L
Go to UniProtKB:  Q9UBL3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
O
76Homo sapiensMutation(s): 1 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GLN
Query on GLN

Download SDF File 
Download CCD File 
K
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
K
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
K
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release