6DCB

Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.998 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE.

Yang, Y.Eichhorn, C.D.Wang, Y.Cascio, D.Feigon, J.

(2019) Nat. Chem. Biol. 15: 132-140


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
7SK snRNA methylphosphate capping enzyme
A
309Homo sapiensMutation(s): 0 
Gene Names: MEPCE (BCDIN3)
EC: 2.1.1.-
Find proteins for Q7L2J0 (Homo sapiens)
Go to Gene View: MEPCE
Go to UniProtKB:  Q7L2J0
Entity ID: 1
MoleculeChainsLengthOrganism
human 7SK RNA stem-loop 1 proximalB36Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.998 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.160 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 118.280α = 90.00
b = 118.280β = 90.00
c = 78.630γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM107567

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Derived calculations
  • Version 1.2: 2019-01-02
    Type: Data collection, Database references
  • Version 1.3: 2019-01-30
    Type: Data collection, Database references