9R6H | pdb_00009r6h

Crystal Structure of the M18BP1 SANTA domain as a EGFP-SANTA-nanobody fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.262 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

M18BP1 valency and a distributed interaction footprint determine epigenetic centromere specification in humans.

Walstein, K.Hill, L.Vogt, D.Oberste-Lehn, L.Janning, P.Vetter, I.R.Pan, D.Musacchio, A.

(2026) EMBO J 45: 1537-1572

  • DOI: https://doi.org/10.1038/s44318-026-00698-z
  • Primary Citation of Related Structures:  
    9R6H

  • PubMed Abstract: 

    The histone H3 variant CENP-A is considered an epigenetic landmark of centromeres. Its deposition reflects cell-cycle-regulated assembly of M18BP1, HJURP, and PLK1 on a divalent MIS18α/β scaffold. The localization determinants of this machinery remain poorly characterized. Here, we report that in human cells, artificial M18BP1 dimerization bypasses MIS18α/β, allowing the identification of at least four determinants of M18BP1 centromere localization. These include the SANTA domain, of which we report the first structure, as well as linear motifs in disordered neighboring regions, of which we characterize the interaction footprint on the CENP-A-associated 16-subunit constitutive centromere-associated network (CCAN). Our observations imply that M18BP1, after dimerization, is necessary and sufficient for centromere localization. Its cell-cycle-dependent dimerization on MIS18α/β promotes initial recognition of a multivalent centromeric assembly of old CENP-A and associated proteins, followed by cooption of PLK1 and HJURP and new CENP-A deposition. Our results shed new light on the determinants of centromere epigenetic inheritance in humans.


  • Organizational Affiliation
    • Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, Dortmund, 44227, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein,Mis18-binding protein 1,Chains: A
A, B
487Homo sapiensMutation(s): 1 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for B6F2F5 (Human enterovirus 71)
Explore B6F2F5 
Go to UniProtKB:  B6F2F5
Find proteins for Q6P0N0 (Homo sapiens)
Explore Q6P0N0 
Go to UniProtKB:  Q6P0N0
PHAROS:  Q6P0N0
GTEx:  ENSG00000129534 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsB6F2F5Q6P0N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
C12
Query on C12
A, B
L-PEPTIDE LINKINGC15 H18 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.262 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.2α = 90
b = 120.28β = 121.28
c = 77.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union951430
German Research Foundation (DFG)GermanyCCR 1430

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 2.0: 2026-02-18
    Changes: Database references, Polymer sequence
  • Version 2.1: 2026-03-11
    Changes: Database references