6IHX

Crystal Structure Analysis of bovine Hemoglobin modified by SNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Quaternary Structure Analysis of a Hemoglobin Core in Hemoglobin-Albumin Cluster.

Morita, Y.Yamada, T.Kureishi, M.Kihira, K.Komatsu, T.

(2018) J Phys Chem B 122: 12031-12039

  • DOI: 10.1021/acs.jpcb.8b10077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A core-shell ensemble of bovine hemoglobin (Hb) and human serum albumin (HSA) is an artificial O <sub>2 </sub> carrier as a red blood cell substitute. This protein particle is created by covalent wrapping of a carbonyl Hb with HSAs: Hb <sup>R </sup>- ...

    A core-shell ensemble of bovine hemoglobin (Hb) and human serum albumin (HSA) is an artificial O 2 carrier as a red blood cell substitute. This protein particle is created by covalent wrapping of a carbonyl Hb with HSAs: Hb R -HSA 3 cluster, where Hb R signifies the use of carbonyl Hb (relaxed (R) state conformation) as a starting material. The Hb R -HSA 3 cluster exhibits high O 2 affinity and low cooperativity. Analysis of the quaternary structure of the central Hb R in the cluster revealed that its high O 2 affinity is attributed to the physically immobile Hb R nucleus. Circular dichroism and UV-vis absorption spectroscopy showed that the structure of deoxy Hb R core closely resembles the R-state. The crystal structure of Lys-modified carbonyl Hb R was superimposed on that of carbonyl Hb. These results imply that chemical modifications of the surface Lys groups and Cys-93(β) of the carbonyl Hb with cross-linking agent interfered in the quaternary structure movement from the R-state to tense (T) state. As expected, coupling of deoxy Hb (T-state) with HSAs yielded Hb T -HSA 3 cluster having low O 2 affinity. The mixing of Hb R -HSA 3 and Hb T -HSA 3 clusters conferred a tailor-made formulation of artificial O 2 carrier with a desired O 2 affinity ( P 50 ).


    Organizational Affiliation

    Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK.,Center for Drug Discovery, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Graduate School of Medical Science and Engineering, College of Life Science and Bioengineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and alan.cartmell2@newcastle.ac.uk.,Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy.,JEM Utilization Center, Human Spaceflight Technology Directorate , Japan Aerospace Exploration Agency (JAXA) , 2-1-1 Sengen , Tsukuba-shi , Ibaraki 305-8505 , Japan.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA.,Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain. Electronic address: adoracion.gomez@uam.es.,Center for Structural Biology, and.,Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A. adha@ufl.edu.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland.,State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000, China.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064 harry@nuvolari.ucsc.edu.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States.,Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: liuzhj@shanghaitech.edu.cn.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Novartis Institutes for Biomedical Research (China), Zhangjiang Hi-Tech Park , Pudong New Area, Shanghai 201203, China.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.,Department of Pathology, The University of Chicago, Chicago, IL, United States.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and jcordero@uthsc.edu.,Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi, 13, 56124 Pisa, Italy; Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045; tatiana.kutateladze@ucdenver.edu.,MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen 361102, P.R. China.,Department of Molecular Physiology and Biophysics, terunaga.nakagawa@vanderbilt.edu.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China. Electronic address: wmxing@sibs.ac.cn.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.,Campus Chemical Instrument Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Biological Chemistry and Pharmacology , The Ohio State University , Columbus , Ohio 43210 , United States.,Committee on Microbiology, The University of Chicago, Chicago, IL, United States.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,University of Chinese Academy of Sciences, Beijing, China.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and.,Department of Food and Nutrition, Duksung Women's University, Seoul, South Korea.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Department of Chemistry, University of Florida, Gainesville, FL, U.S.A.,Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,Umeå Center for Microbial Research, Umeå University, Umeå, Sweden.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Department of Chemistry, Umeå University, Umeå, Sweden.,Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,Department of Physics, Ohio State University, Columbus, OH 43210.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,DiscoveRx Corporation , Fremont, California 94538, United States.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China. Electronic address: wangyc@njau.edu.cn.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,Department of Molecular Physiology and Biophysics.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Department of Biology, Technische Universität Darmstadt, D64287 Darmstadt, Germany.,Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Biochemistry and Molecular Biology and ‡Department of Immunology, Mayo Clinic , Rochester, Minnesota 55905, United States.,Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Daejeon, South Korea.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,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 Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. Electronic address: luigi.messori@unifi.it.,Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093-0378, USA.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China.,Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, C
140Bos taurusMutation(s): 0 
Gene Names: HBA
Find proteins for P01966 (Bos taurus)
Go to UniProtKB:  P01966
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B, D
144Bos taurusMutation(s): 0 
Gene Names: HBB
Find proteins for P02070 (Bos taurus)
Go to Gene View: HBB
Go to UniProtKB:  P02070
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.117α = 90.00
b = 78.132β = 90.00
c = 109.539γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references