7DPH | pdb_00007dph

H-Ras Q61H in complex with GppNHp (state 1) after structural transition by humidity control


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.202 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.202 (DCC) 

Starting Model: experimental
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Literature

Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein.

Matsumoto, S.Taniguchi-Tamura, H.Araki, M.Kawamura, T.Miyamoto, R.Tsuda, C.Shima, F.Kumasaka, T.Okuno, Y.Kataoka, T.

(2021) Biochem Biophys Res Commun 565: 85-90

  • DOI: https://doi.org/10.1016/j.bbrc.2021.05.084
  • Primary Citation Related Structures: 
    7DPH, 7DPJ

  • PubMed Abstract: 

    GTP-bound forms of Ras proteins (Ras•GTP) assume two interconverting conformations, "inactive" state 1 and "active" state 2. Our previous study on the crystal structure of the state 1 conformation of H-Ras in complex with guanosine 5'-(β, γ-imido)triphosphate (GppNHp) indicated that state 1 is stabilized by intramolecular hydrogen-bonding interactions formed by Gln61. Since Ras are constitutively activated by substitution mutations of Gln61, here we determine crystal structures of the state 1 conformation of H-Ras•GppNHp carrying representative mutations Q61L and Q61H to observe the effect of the mutations. The results show that these mutations alter the mode of hydrogen-bonding interactions of the residue 61 with Switch II residues and induce conformational destabilization of the neighboring regions. In particular, Q61L mutation results in acquirement of state 2-like structural features. Moreover, the mutations are likely to impair an intramolecular structural communication between Switch I and Switch II. Molecular dynamics simulations starting from these structures support the above observations. These findings may give a new insight into the molecular mechanism underlying the aberrant activation of the Gln61 mutants.


  • Organizational Affiliation
    • Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.

Macromolecule Content 

  • Total Structure Weight: 19.89 kDa 
  • Atom Count: 1,486 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 171 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase HRas171Homo sapiensMutation(s): 1 
Gene Names: HRASHRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.202 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.202 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.769α = 90
b = 91.769β = 90
c = 121.268γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17K15106

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description