Ribonuclease

From Proteopedia

Revision as of 07:51, 21 December 2014

3D Structures of Ribonuclease

Updated on 21-December-2014

• RNase I

• • 3mwq, 3mwq, 3mx8, 3i67, 3i6f, 3i6h, 3i6j, 3i7w, 3eux, 3euy, 3euz, 3ev0, 3ev1, 3ev2, 3ev3, 3ev4, 3ev5, 3ev6, 3dh5, 2e3w, 2g4w, 2g4x, 2gbq, 2blp, 2blz, 1jvt, 1jvv, 1js0, 1fs3, 1kf2, 1kf3, 1kf4, 1kf5, 1kf7, 1kf8, 1aqp, 1a2w, 1rnw, 1rnz, 1rno, 1rnq, 1rbx, 1ssc, 3srn, 4srn, 1srn, 5rsa, 1afu, 1bel, 1c0b, 1c0c, 1lsq, 1rat, 1rbn, 1rha, 1rhb, 1rnx, 1rny, 1rsm, 1xps, 1xpt, 2g8q, 2rat, 3mzq, 3mzr, 3rat, 3rn3, 4rat, 5rat, 6rat, 7rat, 7rsa, 8rat, 8rsa, 9rat, 9rsa, 3mwr, 4ao1- bRNase I pancreatic - bovine

    
  • 3a1r - bRNase I pancreatic - neutron

    
  • 3i7x, 3i7y, 3fkz, 3fl3, 3dh6, 3di7, 3di8, 3di9, 3dib, 3dic, 2oqf, 3bcm, 3bco, 3bcp, 2nui, 2op2, 1ymn, 1ymr, 1ymw, 2apq, 1izp, 1izq, 1izr, 1kh8, 1c8w, 1eic, 1eid, 1eie, 1dy5, 3rsd, 3rsk, 1ssa, 1ssb,1a5p, 1a5q, 1c9v, 1c9x, 3rsp, 4rsd, 3ql1, 3ql2, 3rh1, 3rid - bRNase I pancreatic (mutant)

    
  • 3lxo, 3jw1, 3djo, 3djp, 3djq, 3djv, 3djx, 3dxg, 3dxh, 2w5g, 2w5i, 2w5k, 2w5l, 2w5m, 3d6o, 3d6p, 3d6q, 3d7b, 3d8y, 3d8z, 2qca, 2g8r, 1z6d, 1z6s, 1u1b, 1w4o, 1w4p, 1w4q, 1wbu, 1o0f, 1jn4, 1jvu, 1f0v, 1ruv, 1rnm, 1rnn, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rnc, 1rnd, 1rob, 1rta, 1rtb,1afk, 1afl, 1eos, 1eow, 1o0h, 1o0m, 1o0n, 1o0o, 1qhc, 1rcn- bRNase I pancreatic + nucleotide
    
  • 6rsa - bRNase I pancreatic + nucleotide - neutron

    
  • 3fl0, 3fl1, 4rsk - bRNase I pancreatic (mutant) + nucleotide
    

  • 2xog, 2xoi, 2q4g, 1dfj, 4g8v, 4g8y, 4g90 - bRNase I pancreatic + inhibitor

    
  • 1rar, 1ras - bRNase I pancreatic fluorescent

  • 2p42, 2p43, 2p44, 2p45 , 2p46, 2p47, 2p48, 2p49, 2p4a, 1bzq, 3qsk - bRNase I + antibody
    
  • 3f8g, 2e0j, 2e0l, 2e0m, 2e0o, 1h8x, 1e21, 1dza - hRNase I pancreatic (mutant) - human

    
  • 2k11 - hRNase I pancreatic - NMR
    

  • 1z7x - hRNase I + inhibitor

    
  • 3ljd, 3ln8, 2vq8, 2vq9 - ZeRNase I – Zebra fish
    
  • 2pqx, 2pqy - EcRNase I
 - Escherichia coli
    
  • 2z70, 2ea1 - EcRNase I + DNA
    

  • 3tsr – mRNase I + inhibitor

• 

 RNase II

• • 2ix0, 2id0 - EcRNase II

    
  • 2ix1 - EcRNase II (mutant)

    
  • 1m58, 1km8, 1km9- BuRNase 2 - Bullfrog

  • 1bc4 - BuRNase 2 - NMR
    

  • 1m07 - BuRNase 2 + DNA
    


  • 2bex - hRNase 2 + RNase inhibitor protein
    
  • 2bzz, 2c01, 2c02, 2c05 - hRNase 2 + inhibitor

• RNase III

• • 2nue, 2nuf, 2nug, 1yyk, 1yyw, 4m2z, 4m30 - AaRNase III + RNA - Aquifex aeolicus
    
  • 2ez6, 1yyo, 1yz9, 1rc7 - AaRNase III (mutant) + RNA 

    
  • 1rc5, 1i4s, 1jfz - AaRNase III N-terminal

    
  • 1z5f - BuRNase III
    
  • 2a11 - MtRNase III - Mycobacterium tuberculosis
    
  • 1o0w - TmRNase III - Thermotoga maritima
    

  • 1t4n, 1t4o - yRNase III – yeast - NMR
    
  • 2lbs - yRNase III RNA-binding domain + RNA – NMR
    
  • 2lup, 4oog - yRNase III RNA-binding domain + RNA
    
  • 2luq - yRNase III RNA-binding domain
    
  • 2kb5 - hRNase 3 - NMR
    

  • 1dyt, 1qmt - hRNase 3

    
  • 1h1h - hRNase 3 + nucleotide
    


  • 2khx – hRNase III
    
  • 3n3w, 3o2r - RNase III nuclease domain – Campylobacter jejuni

• RNase 4

• • 1wdy - hRNase 4

    
  • 2rnf, 1rnf - hRNase 4 + nucleotide
    

  • 1kvz - BuRNase 4 - NMR

• RNase 5

• • 1un3, 1un4, 1un5, 1gv7, 1b1e, 1b1j, 1k59, 1k5a, 1k5b - hRNase 5 (mutant)

    
  • 1ang, 1b1i, 2ang - hRNase 5
    
  • 1awz - hRNase 5 - NMR
    
  • 1a4y - hRNase 5 + RNAse inhibitor
    
  • 1agi - bRNase 5
    
  • 1h53, 1hby - hRNase 5 + phosphate derivative
    
  • 1gio - bRNase 5 - NMR
    
  • 1h53 - hRNase 5 + PO4
    
  • 1h0d - hRNase 5 + antibody
    
  • 3lje - ZeRNase 5
    
  • 2bwk - mRNase 5 + sulfate - mouse
    
  • 2bwl - mRNase 5 + phosphate
    
  • 2j4t - mRNase 5

• RNase 6

• • 1oj1, 1oj8 – BuRNase + nucleotide

• RNase 7

• • 2hky - hRNase 7 - NMR

• RNase A

• • 1rra - RNase A (mutant) – rat
    
  • 4j5z, 4j60, 4j61, 4j62, 4j63, 4j64, 4j65, 4j66, 4j67, 4j68, 4j69, 4j6a, 4mxf, 1rta - bRNase A
    
  • 4k7m - bRNase A (mutant)br />
  • 2aas - bRNase A – NMR
    
  • 4kxh – hRNase A
    
  • 2e33 – bRNase A + F-box only protein 2
    
  • 4l55 – bRNase A + aziru

• RNase B

• • 1rbb – bRNase B
    
  • 1rbj - bRNase B + tetranucleotide

• RNase BA

• • 1x1u, 1x1x, 1x1y, 1b27, 1b2u, 1b3s, 1x1w - BaRNase BA + Barstar (mutant) - Bacillus amyloliquefaciens

    
  • 3da7, 1brs, 1bgs - BaRNase BA + Barstar
    

  • 1b2s, 2za4 - BaRNase BA (mutant) + Barstar (mutant)
    
  • 1brn, 2kf5, 2kf6, 1rnb - BaRNase BA + nucleotide
    
  • 3kch, 2f4y, 2f56, 2f5m, 2f5w - BaRNase BA crosslinked

    
  • 2kf3, 2kf4, 1fw7, 1bnr - BaRNase BA – NMR
    
  • 1yvs, 1b2x, 1a2p, 1bni, 1bnj - BaRNase BA 

    
  • 1b20, 1b21, 1b2z, 1bne, 1bnf, 1bng, 1brh, 1bri, 1brj, 1brk, 1bns, 1brg, 1bsa, 1bsb, 1bsc, 1bsd, 1bse, 1ban, 1bao - BaRNase BA (mutant)



• RNase D

• • 1yt3 - EcRNase D



• RNase E

• • 2vmk, 2c4r, 2bx2 - EcRNase E catalytic domain
    
  • 1slj - EcRNase E S1 domain - NMR
    

  • 1smx, 1sn8 - EcRNase E S1 domain 

    
  • 2vrt, 2c0b - EcRNase E catalytic domain + RNA
    
  • 3h8a – EcRNase E recognition domain + enolase

• RNase F1

• • 1fus, 1fut – GfRNase F1 + nucleotide – Gibberella fujikuroi
    
  • 1rck, 1rcl - GfRNase F1 - NMR

• RNase H

• • 3h7i, 3h8s, 3h8w - T4RNase H (mutant) - Enterobacteria phage T4

    
  • 2ihn - T4RNase H (mutant) + DNA
    

  • 3h8j, 1tfr- T4RNase H
    

  • 4e89 – Rnase H – XMRV
    
  • 2rpi, 1ril - TtRNase H - Thermus thermophilus - NMR
    

  • 1rbr, 1rbs, 1rbt, 1rbu, 1rbv, 2rn2 - EcRNase H
    
  • 1lav, 1law, 1rda, 1rdb, 1rdc - EcRNase H (mutant)
    
  • 1jl2 - EcRNase H /TtRNase H
    

  • 3d0p, 3ey1, 3i8d - BhRNase H (mutant) + DNA - Bacillus halodurans

    
  • 1zbf - BhRNase H (mutant)
    

  • 2r7y, 2g8f, 2g8h, 2g8i, 2g8k, 2g8u, 2g8v, 2g8w, 1zbi, 1zbl, 3twh, 3uld - BhRNase H (mutant) + RNA + DNA
    


  • 4htu, 4hue, 4huf, 4hug - BhRNase H (mutant) + DNA
    
  • 4ibn – uRNase H – uncultured
    
  • 4h8k – uRNase H + RNA + DNA

• RNase HI

• • 2qk9, 2qkb, 2qkk - hRNase HI (mutant) + RNA + DNA
    

  • 3h08 - RNase HI - Chlorobaculum tepidum
    
  • 3aa2, 3aa3, 3aa4, 3aa5, 2yv0, 2z1g, 2z1h, 2z1i, 2z1j, 1wse, 1wsf, 1wsg, 1wsh, 1wsi, 1wsj, 1jxb, 1jl1, 1f21, 1kva, 1kvb, 1kvc, 1goa, 1gob, 1goc - EcRNase HI (mutant)
    

  • 1g15, 1rdd, 1rnh - EcRNase HI

    
  • 1rch - EcRNase HI - NMR
    

  • 2zqb - SoRNase HI (mutant) - Shewanella oneidensis
    
  • 2e4l - SoRNase HI
    

  • 3bsu - hRNase HI catalytic domain + RNA + DNA
    

  • 2ehg - RNase HI - Sulfolobus tokodaii
    

  • 1qhk - yRNase HI N-terminal – NMR
    
  • 3u3g – RNase HI – uncultured organism
    
  • 4e19, 4nyn – RNase HI – Halobacterium salinarium

• RNase HII

• • 3p83 - AfRNase HII + DNA polymerase sliding clamp - Archaeoglobus fulgidus

    
  • 1i39, 1i3a - AfRNAse HII

    
  • 3puf, 3p56, 3p5j - hRNAse H2 subunits α+β+γ 

    
  • 3kio - mRNase H2 subunits α+β+γ 
- mouse

    
  • 3o3g - TmRNase HII + DNA
    

  • 3o3f, 3o3h, 4hht - TmRNase HII (mutant) + DNA
    
  • 2etj - TmRNase HII 

    
  • 1x1p, 1io2 - TkRNase HII

    
  • 2dfe, 2dff, 2dfh - TkRNase HII (mutant) - Thermococcus kodakarensis

    
  • 1eke - RNase HII - Methanocalcococcus jannaschii



• RNase HIII

• • 2d0a, 2d0b, 2d0c - GsRNase HIII - Geobacillus stearothermophilus


    
  • 3asm - GsRNase HIII (mutant)
    
  • 1uax - PhRNase HIII – Pyrococcus horikoshii
    
  • 3vn5 - AaRNase HIII

• RNase J

• • 3bk1 - TtRNase J

    
  • 3bk2 - TtRNase J + nucleotide
    
  • 3zq4 - BsRNase J1- Bacillus subtilis

• RNase L

• • 4o1o - pRNase L + oligoadenylate + CMP – pig
    
  • 4o1p - pRNase L + oligoadenylate + AMPPNP
    
  • 4oav - hRNase L + oligoadenylate + AMPPCP + RNA

• RNase LE

• • 1dix - RNase LE - tomato

• RNase MAR1

• • 1xn4 - RNase MAR1 – Leishmania major
    
  • 2b34 - RNase MAR1 – Caenorhabditis elegans

• RNase MS

• • 1rms, 1rds - RNase MS + nucleotide - Aspergillus phoenicis

• RNase MC1

• • 1v9h, 1j1f, 1j1g - McRNase MC1 (mutant) + nucleotide - Momordica charantia 

    
  • 1ucg - McRNase MC1 (mutant)
    
  • 1ucd, 1uca, 1ucc - McRNase MC1 + nucleotide
    
  • 1bk7 - McRNase MC1



• RNase NT

• • 1vcz, 1vd1, 1vd3 - toRNase NT + nucleotide - tobacco 


    
  • 1iyb - toRNase NW

• RNase P

• • 3ok7, 3okb, 3q1q, 3q1r - TmRNase P + TmRNase P RNA + tRNA Phe

    
  • 1nz0 - TmRNase P

    
  • 1d6t - RNase P - Staphylococcus aureus
    
  • 2a64 - BsRNase P (mutant) - Bacillus stearothermophilus


    
  • 1a6f, 1nbs, 2jg4 - BsRNase P (mutant)
    
  • 1ts9, 1tsf – AfRNase P
    
  • 1u9s – RNase P – synthetic
    
  • 2avs - PfRNase P (mutant) – Pyrococcus furiosus
    
  • 2k3r, 2ki7 - PfRNase P
    
  • 2ljp – EcRNase P
    
  • 2av5 - PhRNase P component 2
    
  • 1x0t - PhRNase P component 4
    
  • 2zae - PhRNase P component 1 and 4
    
  • 2czv - PhRNase P component 2 (mutant) and 3
    
  • 2cvz, 2zae – PhRNase P
    
  • 3iab – yRNase P subunits POP6 POP7 + RNase MRP P3 domain

• RNase PH

• • 3dd6 - RNase PH - Bacillus anthracis

    
  • 1oyp, 1oyr, 1oys - BsRNase PH 

    
  • 1r6l, 1r6m - PaRNase PH - Pseudomonas aeruginosa

    
  • 3b4t - MtRNase PH - Mycobacterium tuberculosis 

    
  • 1udn - AaRNase PH

    
  • 1udo, 1udq, 1uds - AaRNase PH (mutant)



• RNase RH

• • 1bol – Rhizopus niveus

• RNase S

• • 3oqy, 3oqz, 3or0, 1z3l, 1z3m, 1z3p, 1y92, 1y94, 1fev, 1d5d, 1d5e, 1d5h, 2rln, 1qwq, 4n4c - bRNase S seminal (mutant)

    
  • 1tq9, 1r5c, 11ba, 11bg - bRNase S + nucleotide
    

  • 1r5d, 1r3m, 1n1x, 1n3z, 1j7z, 1j80, 1j81, 1j82, 1cjq, 1cjr, 1bsr,1rbc, 1rbd, 1rbe, 1rbf, 1rbg, 1rbh, 1rbi, 1rnu, 1rnv, 2rns - bRNase S

    
  • 1b6v - bRNase S/bRNase A

• RNase S3

• • 1iqq - RNase S3 - Japanese pear

• RNase SA

• • 3a5e, 1zgx, 1ynv, 1t2h, 1t2i, 1uci, 1ucj, 1uck, 1ucl, 1i70, 1i8v, 1box, 4gho - SaRNase SA guanyl-specific (mutant) - Streptomyces aureofaciens

    
  • 1lni,1c54, 1rge, 1rgf, 1rgg, 1rgh, 1sar - SaRNase SA
    
  • 1gmp, 1gmq, 1gmr, 2sar - SaRNase SA +nucleotide
    

  • 1ay7 - SaRNase SA + Barstar
    
  • 1rsn - SaRNase SA + cyclophosphothiolate

• RNase SA2

• • 1py3, 1pyl - SaRNase SA2
    
  • 3dgy, 3dh2, 3d4a, 3d5g, 3d5i - SaRNase SA2 + mononucleotide

• RNase SA3

• • 1mgr, 1mgw - SaRNase SA3

• RNase SF11

• • 1ioo - RNase SF11 - Nicotiana alata



• RNase T

• • 2is3 - EcRNase T

    
  • 2f96 - PaRNase T
    
  • 3ngy – EcRNase T (mutant) + His tag
    
  • 3ngz - EcRNase T (mutant) + nucleotide
    
  • 3nh0, 3nh1, 3nh2 - EcRNase T + nucleotide
    
  • 3v9s, 3v9u, 3v9w, 3v9x, 3v9z, 3va0, 3va3, 4kaz, 4kb0, 4kb1 - EcRNase T + DNA

• RNase T1

• • 1tto,1rn1, 1rn4, 1rnt, 2aad, 2aae - AoRNase T1 - Aspergillus oryzae 

    
  • 1q9e, 1iyy, 1i2e, 1i2f, 1i2g, 1i3f, 1i3i, 1hz1, 1fys, 1fzu, 1ch0, 4bir, 3bir, 5bir,1g02, 1hyf, 1trp, 1trq, 2bir, 4rnt, 5rnt, 6rnt, 7rnt , 8rnt, 9rnt - AoRNase T1 (mutant)
    
  • 1lov, 1low, 1loy, 1i0v, 1i0x, 1b2m, 1rhl, 1bir, 1rgk, 1rgl - AoRNase T1 (mutant) + nucleotide
    
  • 1bvi, 2bu4, 2hoh, 4hoh, 5hoh, 3hoh, 2gsp, 3gsp, 4gsp, 5gsp, 6gsp, 7gsp, 1gsp, 1det, 1rls, 1lra, 1rga,1bu4, 1rgc, 2rnt, 3bu4, 4bu4, 5bu4, 3syu, 3urp - AoRNase T1 + nucleotide
    

  • 3rnt - AoRNase T1 + V
    
  • 1ygw - AoRNase T1 – NMR

• RNase T2

• • 3t0o – hRNase T2

• RNase U2

• • 3agn, 3ago, 3ahw - UsRNase U2 + AMP - Ustilago sphaerogena

    
  • 1rtu - UsRNase U2

• RNase U2B

• • 3ahs - UsRNase U2B

• RNase Z

• • 2e7y - TmRNase Z
    
  • 2fk6, 4gcw - BsRNase Z (mutant) + tRNA Thr
    

  • 1y44 - BsRNase Z (mutant)
    
  • 2cbn – EcRNase Z
    
  • 3v32, 3v33, 3v34 – hRNase Z

• α-sarcin

• • 1de3 - αsRNase – Aspergillus giganteus
    
  • 1r4y - αsRNase (mutant)

• Oligoribonuclease

• • 2igi, 1yta – EcORNase
    
  • 2gbz - ORNase - Xanthomonas campestris
    
  • 1j9a - ORNase - Haemophilus influenzae
    
  • 3tr8 – ORNase – Coxiella burnetii

• Polynucleotide Phosphorylase

• • 3cdi - EcPNPase
    
  • 3gll - EcPNPase core
    
  • 3cdj - EcPNPase C-terminal truncated
    
  • 1e3h, 1e3p - PNPase - Streptomyces antibioticus
    
  • 3gcm, 3gme, 3h1c - EcPNPase + RNase E recognition domain
    
  • 3h36 - PNPase fragment - Streptococcus mutans

• Binase

• • 1gou, 1gov, 1goy – BiBinase – Bacillus intermedius
    
  • 2rbi, 4haa – BiBinase (mutant)
    
  • 1buj – BiBinase – NMR

• Poly(A)-specific RNase

• • 1ug8 – mParn R3H domain - NMR
    
  • 1whv – mParn RNA-binding domain - NMR
    
  • 2rok - mParn CAP-binding domain - NMR
    
  • 3d45 - mParn + nucleotide
    
  • 2a1s - hParn
    
  • 2a1r, 3ctr – hParn + nucleotide
    
  • 2zpo – RNase – Chelonia mydas
    
  • 3a4y, 3idz, 3ie0, 3ie2 – TtRNase (mutant) – Thermus thermophilus
    
  • 3iek - TtRNase
    
  • 3ie1, 3iem - TtRNase (mutant) + RNA
    
  • 3iel - TtRNase + nucleotide
    
  • 4b8a – yRNase pop2 + cell division cycle protein 39
    
  • 4b8c – yRNase pop2 + cell division cycle protein 39 + CCR4

}}

References

1. ↑ Birdsall DL, McPherson A. Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A. J Biol Chem. 1992 Nov 5;267(31):22230-6. PMID:1429575

• Created with the participation of David S. Goodsell, Eric Martz, and Eran Hodis.