5W1G

CR1-07 unliganded Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.

Clark, L.E.Mahmutovic, S.Raymond, D.D.Dilanyan, T.Koma, T.Manning, J.T.Shankar, S.Levis, S.C.Briggiler, A.M.Enria, D.A.Wucherpfennig, K.W.Paessler, S.Abraham, J.

(2018) Nat Commun 9: 1884-1884

  • DOI: 10.1038/s41467-018-04271-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in s ...

    While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1-Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Department of biological and medical physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.,Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina. Electronic address: jromero@fcq.unc.edu.ar.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Plant Pathology, Nanjing Agriculture University, 210095 Nanjing, China.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France. pedro.alzari@pasteur.fr marco.bellinzoni@pasteur.fr.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: jrmarszalek@mdanderson.org.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: patrick@salk.edu.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: ysun8@mdanderson.org.,Center for Open Research Resources & Equipment (COR2E) , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina.,Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287.,Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN 46202, USA.,Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA.,Institute for X-Ray Physics, University of Goettingen, 37077 Goettingen, Germany.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.,3Faculty of Health Sciences, Department of Medical Biology, Research group of Host-Microbe Interactions, UiT-The Artic University of Norway, 9037 Tromsø, Norway.,Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Institute of Molecular and Cell Biology, Singapore 138673.,Department of Molecular and Cellular Biology , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,6Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University, Shanghai, People's Republic of China.,Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. rficner@uni-goettingen.de.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. Electronic address: smeroueh@iu.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: margaret.phillips@utsouthwestern.edu.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK katrin.rittinger@crick.ac.uk.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea. jylee001@dongguk.edu.,School of Molecular Sciences, Arizona State University, Tempe, AZ 85287.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea. Electronic address: hscho8@yonsei.ac.kr.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore. julien@ntu.edu.sg.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA.,Department of Microbiology, Monash University, Clayton, Australia.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,Department of Physics, Arizona State University, Tempe, AZ 85287.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,5Department of Integrative Medical Biology (IMB), Umeå University, SE-90187 Umeå, Sweden.,Department of Pharmaceutical Sciences , University of Connecticut , 69 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Center for Plant Cell Biology, University of California, Riverside, CA 92521.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. nyan@princeton.edu.,Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. sjohann1@gwdg.de.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. pneuman2@gwdg.de.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China. Electronic address: lugw@scu.edu.cn.,National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China. Electronic address: Jianggu2012@163.com.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea. Electronic address: hanc210@snu.ac.kr.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.,4Umeå Centre for Molecular Medicine (UCMM), Umeå University, SE-90187 Umeå, Sweden.,Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.,Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore. julien@ntu.edu.sg.,1Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90187 Umeå, Sweden.,Department of Biological Sciences Xi'an Jiaotong-Liverpool University111 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou, 215123, People's Republic of China.,Laboratory of biomolecular NMR spectroscopy, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,2Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.,SLAC National Accelerator Laboratory, Menlo Park, CA 94025.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461; denis.rousseau@einstein.yu.edu.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Hauptman-Woodward Institute and SUNY University of Buffalo, Buffalo, NY 14203.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Department of Chemistry , University of Connecticut , 55 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China; Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China.,Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CR1-07 Fab heavy chain
H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CR1-07 Fab light chain
L
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.770α = 90.00
b = 137.410β = 148.66
c = 78.670γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
BALBESphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAI007061
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAI109740
National Institutes of Health/National Institute of General Medical SciencesUnited StatesDP5OD023084
Other privateUnited States--
Other privateUnited States--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release