5UK9

Wild-type K-Ras(GCP) pH 6.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.887 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D.

Parker, J.A.Volmar, A.Y.Pavlopoulos, S.Mattos, C.

(2018) Structure 26: 810

  • DOI: 10.1016/j.str.2018.03.018

  • PubMed Abstract: 
  • Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of ...

    Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of the GTPase not in complex with other proteins. We present the crystal structure of wild-type K-Ras bound to the GTP analog GppCH 2 p, with K-Ras in the state 1 conformation. Signatures of conformational states obtained by one-dimensional proton NMR confirm that K-Ras has a more substantial population of state 1 in solution than H-Ras, which predominantly favors state 2. The oncogenic mutant K-RasG12D favors state 2, changing the balance of conformational states in favor of interactions with effector proteins. Differences in the population of conformational states between K-Ras and H-Ras, as well as between K-Ras and its mutants, can provide a structural basis for focused targeting of the K-Ras isoform in cancer-specific strategies.


    Organizational Affiliation

    PRESTO, JST, Nagoya 464-8601, Japan.,ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan.,Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India.,Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan.,Vollum Institute, Oregon Health & Science University, Portland, United States.,Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.,School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. shi-lab@tsinghua.edu.cn.,Division for Structural Biochemistry, OE8830, Hannover Medical School, Hannover, Germany.,Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, United States.,Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.,Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA.,Cell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji-shi, Japan.,School of Pharmacy , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania. Electronic address: siksnys@ibt.lt.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: c.mattos@northeastern.edu.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China. shi-lab@tsinghua.edu.cn.,Centre for Structural Systems Biology (CSSB), German Electron Synchrotron (DESY), Hamburg, Germany.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, 430072, Wuhan, China.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England.,Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India tpsingh.aiims@gmail.com.,Department of Biology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Chemistry, College of Science , University of Hail , Saudi Arabia.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. huangchh@shsmu.edu.cn.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China. leim@shsmu.edu.cn.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: d.wigley@imperial.ac.uk.,Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, England.,Institute for Biophysical Chemistry, OE4350, Hannover Medical School, Hannover, Germany.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Chemistry and Biochemistry , Laurentian University , Sudbury , Ontario , Canada P3E 2C6.,Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.,Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. huangchh@shsmu.edu.cn.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia. Electronic address: jesus.fernandez2@universidadeuropea.es.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.,Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan.,Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China.,Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui-shi, Japan.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. leim@shsmu.edu.cn.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London W12 0BZ, England.,Department of Applied Chemistry, Waseda University, Tokyo 169-8555, Japan.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. leim@shsmu.edu.cn.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
166Homo sapiensMutation(s): 0 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GCP
Query on GCP

Download SDF File 
Download CCD File 
B
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.887 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.107α = 90.00
b = 87.553β = 90.00
c = 93.692γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-3000data collection
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1517295

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references
  • Version 1.2: 2018-06-20
    Type: Data collection, Database references