8RB2 | pdb_00008rb2

The crystal structure of DNA-bound human MutSbeta (MSH2_E749A/MSH3_E976A) in the canonical mismatch bound conformation with ADP bound in MSH2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 
    0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3

Thomsen, M.Neudegger, T.Thieulin-Pardo, G.Blaesse, M.Costanzi, E.Steinbacher, S.Plotnikov, N.V.Dominguez, C.Iyer, R.R.Wilkinson, H.A.Monteagudo, E.Haque, T.S.Prasad, B.C.Finley, M.Boudet, J.Vogt, T.F.Felsenfeld, D.P.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein Msh2
A, E
934Homo sapiensMutation(s): 1 
Gene Names: MSH2
UniProt & NIH Common Fund Data Resources
Find proteins for P43246 (Homo sapiens)
Explore P43246 
Go to UniProtKB:  P43246
PHAROS:  P43246
GTEx:  ENSG00000095002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43246
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA mismatch repair protein Msh3
B, F
1,137Homo sapiensMutation(s): 1 
Gene Names: MSH3
UniProt & NIH Common Fund Data Resources
Find proteins for P20585 (Homo sapiens)
Explore P20585 
Go to UniProtKB:  P20585
PHAROS:  P20585
GTEx:  ENSG00000113318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20585
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*GP*G)-3')
C, G
24synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*GP*G)-3')
D, H
24synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
HA [auth E],
I [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PEG
Query on PEG

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T [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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AB [auth H]
BA [auth B]
EA [auth B]
FA [auth B]
IA [auth E]
AB [auth H],
BA [auth B],
EA [auth B],
FA [auth B],
IA [auth E],
JA [auth E],
NA [auth E],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
TA [auth E],
U [auth B],
VA [auth F],
WA [auth F],
XA [auth F],
Y [auth B],
Z [auth B],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
GA [auth D]
J [auth A]
K [auth A]
CA [auth B],
DA [auth B],
GA [auth D],
J [auth A],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
Q [auth A],
R [auth A],
S [auth B],
UA [auth F],
V [auth B],
W [auth B],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A],
SA [auth E],
YA [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.612α = 110.03
b = 104.29β = 91.72
c = 121.069γ = 110.21
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CHDI FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Structure summary