5ZM5

Crystal structure of human ORP1-ORD in complex with cholesterol at 2.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P2/PI(3,4)P2.

Dong, J.Du, X.Wang, H.Wang, J.Lu, C.Chen, X.Zhu, Z.Luo, Z.Yu, L.Brown, A.J.Yang, H.Wu, J.W.

(2019) Nat Commun 10: 829-829

  • DOI: 10.1038/s41467-019-08791-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs), and ORP1L specifically localizes to LELs. Here, we show in vitro that ORP1 is a PI(4,5)P <sub>2 </sub>- or PI(3,4)P <sub ...

    Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs), and ORP1L specifically localizes to LELs. Here, we show in vitro that ORP1 is a PI(4,5)P 2 - or PI(3,4)P 2 -dependent cholesterol transporter, but cannot transport any PIPs. In cells, both ORP1L and PI(3,4)P 2 are required for the efficient removal of cholesterol from LELs. Structures of the lipid-binding domain of ORP1 (ORP1-ORD) in complex with cholesterol or PI(4,5)P 2 display open conformations essential for ORP function. PI(4,5)P 2 /PI(3,4)P 2 can facilitate ORP1-mediated cholesterol transport by promoting membrane targeting and cholesterol extraction. Thus, our work unveils a distinct mechanism by which PIPs may allosterically enhance OSBP/ORPs-mediated transport of major lipid species such as cholesterol.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: chenzhongzhou@cau.edu.cn.,Center of Biomedical Analysis, Tsinghua University, 100084, Beijing, China.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas , Universidade Federal de Minas Gerais , Av. Antônio Carlos , 6627 Belo Horizonte , Brazil.,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, 116034, Dalian, China. duming@dlpu.edu.cn.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China. gzhao@cau.edu.cn.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 7990 Enterprise Street, Burnaby, BC V5A 1V7, Canada.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA. dlloyd@amgen.com.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Amgen Research, Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia. h.rob.yang@unsw.edu.au.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia.,Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista , Rua Cristóvão Colombo , 2265 São José do Rio Preto , Brazil.,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Departamento de Microbiología, Facultad de Salud , Universidad del Valle , Calle 4B No. 36-00 Cali , Colombia.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. jiaweiwu@suda.edu.cn.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China. jiaweiwu@suda.edu.cn.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Amgen Research, Comparative Biology and Safety Sciences, Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterol-binding protein-related protein 1
A
426Homo sapiensMutation(s): 0 
Gene Names: OSBPL1A (ORP1, OSBP8, OSBPL1, OSBPL1B)
Find proteins for Q9BXW6 (Homo sapiens)
Go to Gene View: OSBPL1A
Go to UniProtKB:  Q9BXW6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.803α = 90.00
b = 135.803β = 90.00
c = 91.154γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0502004

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references