CC-BY-3.0 David S. Goodsell and the RCSB PDB
`
`DNA: storing and reading
`genetic information
`84. DNA 1bna
`85. Restriction Endonuclease
`EcoRI 1eri
`86. DNA Photolyase 1tez
`87. Topoisomerase 1a36
`88. RNA Polymerase 2e2i
`89. lac Repressor 1lbh 1efa
`90. Cataabolite Gene Activator
`Protein 1cgp
`91. TATA-binding Protein/
`Transcription Factor IIB 1ais
`92. DNA Helicase 4esv
`93. DNA Polymerase 1tau
`94. Nucleosome 1aoi
`95. HU Protein 1p51
`96. Single-stranded
`DNA-binding Protein 3a5u
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`84
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`85
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`86
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`87
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`71
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`74
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`89
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`88
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`90
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`Protein Synthesis: building
`new molecular machines
`67. Transfer RNA 4tna
`68. Valyl-tRNA Synthetase 1gax
`69. Threonyl-tRNA Synthetase 1qf6
`70. Glutaminyl-tRNA Synthetase1euq
`71. Isoleucyl-tRNA Synthetase 1ffy
`72. Phenylalanyl-tRNA Synthetase 1eiy
`73. Aspartyl-tRNA Synthetase 1asy
`74. Ribosome 1j5e, 1jj2
`75. Elongation Factor Tu/tRNA 1ttt
`76. Elongation Factor G 1dar
`77. Elongation Factor Ts and Tu 1efu
`78. Prefoldin 1fxk
`79. Chaperonin GroEL/ES 1aon
`80. Proline cis/trans Isomerase 2cpl
`81. Heat Shock Protein Hsp90 2cg9
`82. Proteasome 4b4t
`83. Ubiquitin 1ubq
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`67
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`69
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`70
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`68
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`72
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`73
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`75
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`76
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`65
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`63
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`Infrastructure:
`supporting and
`moving cells
`
`63. Actin 1m8q
`64. Myosin 1m8q
`65. Microtubule1tub
`66. Collagen 1bkv
`(far left)
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`64
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`Molecular Machinery:
`Molecular Machinery:
`A Tour of the Protein Data Bank
`A Tour of the Protein Data Bank
`
`rcsb.org
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`30
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`31
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`36
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`37
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`Cells build many complex molecular machines that perform the biological jobs needed for life. Some of these machines
`are molecular scissors that cut food into digestible pieces. Others then use these pieces to build new molecules when
`cells grow or tissues need to be repaired. Some molecular machines form sturdy beams that support cells, and others are
`motors that use energy to crawl along these beams. Some recognize attackers and mobilize defenses against infection.
`
`Adenosine
`Triphosphate
`(ATP)
`
`Glucose
`
`Water
`
`Researchers around the world are studying these molecules at the atomic level. These 3D structures are
`freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. A few
`examples from the ~100,000 structures held in the PDB are shown here at a magnification of about
`3,500,000 times, with each atom represented as a small sphere. The enormous range of molecular sizes is
`illustrated here, from the water molecule (H2O) with only three atoms (shown at the left) to the ribosomal
`subunits with hundreds of thousands of atoms.
`
`1
`
`Digestive Enzymes: breaking food
`into small nutrient molecules
`1. Amylase 1smd
`5. Pepsin 5pep
`2. Phospholipase 1poe
`6. Trypsin 2ptc
`3. Deoxyribonuclease 2dnj
`7. Carboxypeptidase 3cpa
`4. Lysozyme 1lz1
`8. Ribonuclease 5rsa
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`2
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`3
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`4
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`5
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`6
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`7
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`8
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`Blood Plasma Proteins: transporting nutrients
`and defending against injury
`9. Factor X 1xka, 1iod
`11. Fibrin 1m1j, 2baf
`10. Thrombin 1ppb
`12. Serum Albumin 1e7i
`
`Viruses and Antibodies: engaging in
`constant battle in the bloodstream
`13. Antibody 1igt
`14. Rhinovirus 4rhv
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`9
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`10
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`Hormones: carrying molecular
`messages through blood
`15. Glucagon 1gcn
`16. Insulin 2hiu
`17. Epidermal Growth Factor 1egf
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`15
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`16
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`17
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`11
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`12
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`13
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`14
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`32
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`Energy Production:
`powering the processes
`of the cell
`30. Cytochrome c Oxidase
`(Complex IV) 1oco
`31. Cytochrome c 3cyt
`32. Cytochrome bc1
`(Complex III) 1bgy
`33. Succinate Dehydrogenase
`(Complex II) 1nek
`34. NADH-Quinone Oxidoreductase
`(Complex I) 3m9s, 3rko
`35. ATP Synthase 1e79, 1c17, 1l2p, 2a7u
`36. Myoglobin 1mbd
`37. Hemoglobin 4hhb
`
`Storage: containing nutrients
`for future consumption
`38. Ferritin 1hrs
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`33
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`34
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`35
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`38
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`Channels, Pumps and Receptors: getting
`back and forth across the membrane
`18. Ras Protein 5p21
`19. Beta2-Adrenergic Receptor/Gs Protein 3sn6
`20. Acetylcholine Receptor 2bg9
`21. Epidermal Growth Factor Receptor
`1ivo, 2jwa, 2gs6
`22. Rhodopsin 1f88
`23. P-glycoprotein 4m2t
`24. Potassium Channel 3lut
`25. Calcium Pump 1su4
`26. Cyclooxygenase 1prh
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`19
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`20
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`18
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`39
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`Photosynthesis:
`harvesting
`energy from
`the sun
`27. Photosystem II
`1s5l
`28. Light-harvesting
`Complex 1rwt
`29. Photosynthetic
`Reaction
`Center 1prc
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`66
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`27
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`28
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`40
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`41
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`42
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`29
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`Scale:
`1nm
`
`5nm
`
`10nm
`
`1nm (nanometer) =
`10-6 millimeters
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`21
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`43
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`44
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`45
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`46
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`22
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`23
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`24
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`25
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`26
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`53
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`Enzymes: cutting and joining the molecules of life
`55
`53. Hexokinase 1dgk
`39. Fatty Acid Synthase 2uvb, 2uvc
`54. Phosphoglucose Isomerase 1hox
`40. RuBisCo: Ribulose Bisphosphate
`Carboxylase/Oxygenase 1rcx
`55. Phosphofructokinase 4pfk
`41. Green Fluorescent Protein 1gfl
`56. Aldolase 4ald
`42. Luciferase 2d1s
`57. Triosephosphate Isomerase 2ypi
`43. Glutamine Synthetase 2gls
`58. Glyceraldehyde-3-phosphate
`Dehydrogenase 3gpd
`44. Alcohol Dehydrogenase 2ohx
`59. Phosphoglycerate Kinase 3pgk
`45. Dihydrofolate Reductase 1dhf
`60. Phospoglycerate Mutase 3pgm
`46. Nitrogenase 1n2c
`61. Enolase 5enl
`47. Leucine Aminopeptidase 1lap
`62. Pyruvate Kinase 1a3w
`48. beta-Lactamase 4blm
`49. Catalase 1qqw
`50. Thymidylate Synthase 2tsc
`51. Tryptophan Synthase 1wsy
`52. Aspartate Carbamoyltransferase 4at1
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`51
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`58
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`48
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`50
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`47
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`52
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`49
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`91
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`78
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`79
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`80
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`92
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`77
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`81
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`82
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`94
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`93
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`95
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`93
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`96
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`54
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`56
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`59
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`60
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`57
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`61
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`Extracellular Proteins
`
`Membrane Proteins
`
`Intracellular Proteins: Cytosol
`
`Intracellular Proteins: Cytosol
`
`Intracellular Proteins: Nucleus
`
`SANOFI v. GENENTECH
`IPR2015-01624
`EXHIBIT 2084