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- PDB-8af0: Crystal structure of human angiogenin and RNA duplex -

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Basic information

Entry
Database: PDB / ID: 8af0
TitleCrystal structure of human angiogenin and RNA duplex
Components
  • Angiogenin
  • RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3')
KeywordsRNA BINDING PROTEIN / ribonuclease / RNA duplex / RNase A-like
Function / homology
Function and homology information


angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation ...angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / positive regulation of phosphorylation / endocytic vesicle / RNA nuclease activity / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / peptide binding / RNA endonuclease activity / placenta development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cell migration / heparin binding / actin cytoskeleton / chromosome / ribosome binding / actin binding / growth cone / angiogenesis / endonuclease activity / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / receptor ligand activity / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / negative regulation of apoptotic process / nucleolus / signal transduction / protein homodimerization activity / extracellular space / DNA binding / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
RNA / RNA (> 10) / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSievers, K. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structure of angiogenin dimer bound to double-stranded RNA.
Authors: Sievers, K. / Ficner, R.
History
DepositionJul 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3')
D: RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3')
A: Angiogenin
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6928
Polymers40,3234
Non-polymers3684
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.380, 66.660, 101.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 18 or resid 20...
d_2ens_1(chain "B" and (resid 4 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROC4 - 18
d_12ens_1GLYHISC20 - 65
d_13ens_1GLULEUC67 - 83
d_14ens_1GLYTYRC85 - 94
d_15ens_1ALAPROC96 - 123
d_21ens_1SERPROH4 - 18
d_22ens_1GLYHISH20 - 65
d_23ens_1GLULEUH67 - 83
d_24ens_1GLYTYRH85 - 94
d_25ens_1ALAPROH96 - 123

NCS oper: (Code: givenMatrix: (-0.998973440212, -0.0438681003476, 0.011298474349), (0.0446947253707, -0.995109235536, 0.0880908103925), (0.00737883966214, 0.088505362117, 0.996048369108)Vector: -52. ...NCS oper: (Code: given
Matrix: (-0.998973440212, -0.0438681003476, 0.011298474349), (0.0446947253707, -0.995109235536, 0.0880908103925), (0.00737883966214, 0.088505362117, 0.996048369108)
Vector: -52.1048168718, 33.2077947212, -17.8744292545)

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Components

#1: RNA chain RNA (5'-R(*GP*CP*CP*CP*GP*CP*CP*UP*GP*UP*CP*AP*CP*GP*CP*GP*GP*GP*C)-3')


Mass: 6059.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14101.967 Da / Num. of mol.: 2 / Mutation: H114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli (E. coli)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM NaCl, 20 % (w/v) PEG6000, 100 mM Hepes pH 7.0
Temp details: Incubation of plate for 20 days at 293.15 K, then for 8 days at 277.15 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.43→45.12 Å / Num. obs: 24805 / % possible obs: 99.8 % / Redundancy: 7.088 % / Biso Wilson estimate: 70.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.03
Reflection shellResolution: 2.43→2.53 Å / Mean I/σ(I) obs: 1.49 / Num. unique obs: 2830 / CC1/2: 0.694 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PHENIX1.20.1refinement
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOP

5eop


Resolution: 2.43→45.12 Å / SU ML: 0.3772 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 663 4.99 %
Rwork0.2051 12625 -
obs0.2083 13288 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.85 Å2
Refinement stepCycle: LAST / Resolution: 2.43→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 800 24 60 2851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982923
X-RAY DIFFRACTIONf_angle_d1.44254119
X-RAY DIFFRACTIONf_chiral_restr0.072468
X-RAY DIFFRACTIONf_plane_restr0.012402
X-RAY DIFFRACTIONf_dihedral_angle_d13.131229
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.77367197012 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.620.381320.3332467X-RAY DIFFRACTION99.43
2.62-2.880.37841300.29122484X-RAY DIFFRACTION99.35
2.88-3.30.32551290.25752475X-RAY DIFFRACTION98.56
3.3-4.160.28371320.2022531X-RAY DIFFRACTION98.96
4.16-45.120.22241400.16712668X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.85607774944-0.2128100676111.580502990894.53719759545-4.064211763793.57542605629-0.165109600602-0.6058316473050.1217024927011.047876278930.2444657068350.085591598017-0.815065603996-0.11528948858-0.07609187529421.0760700260.01927266240470.01278276842071.0757247826-0.1227956421680.538193093011-13.3270596293-0.153520866285-25.7396048196
28.80130030924-0.822744324604-3.382734929693.024468909184.539417076572.05326334788-0.527148924902-0.492773064677-0.4793621765040.9699538500270.0125411132242-0.3169957043743.644305200052.460138121120.1496186362971.408425694190.267382894381-0.050565674361.03114848298-0.07597296458270.675631087011-9.628529636992.85615510171-5.90243437345
32.08943782276-1.598614074030.4813320828594.022860972442.501874296263.95124413053-0.591945248348-1.98520646912-0.903577239466-1.154779532260.19774365362-0.3403975788750.890571293331.51853057240.2039691776011.043250593570.1071060328030.1687692911611.208676859010.1700915024840.845632263132-23.1548918493-0.5599810416696.46484017871
45.94435758103-5.999056185313.576382474737.18734735929-4.371357579252.73633259945-0.04046793578820.166712050489-1.31486312838-1.272166653441.055633157321.069728257140.195846794375-0.474916663145-0.6443089761241.073690335130.0441454436134-0.1563603530131.12359717270.009069836457350.828146213393-19.55709429-6.48031913221.6671114776
58.05388641907-4.474921330073.100433821285.42046264662-0.6112038879792.952569779620.722339500791.7492033247-0.233555776997-0.614658008966-0.5069035171230.4233921337471.041371796240.879926333198-0.06043348140721.571513822090.149927901098-0.07422340704990.937378577688-0.08702982370820.579902058506-15.65547942414.51383441864-12.1303827365
63.58440658896-4.08654881491-1.902372924894.695646425032.252023251336.61064683686-0.0251603474198-0.3530784467490.651817666390.09710035690570.834530947771-0.877186827776-2.283860687022.69323298871-0.5372847883481.06124524816-0.1122972125840.03665030778811.34123942054-0.1130881347260.731819963931-7.82697740453-3.86929463205-26.7611679572
79.57315617879-3.604129557922.700851787634.56433643896-4.002626471923.469280276420.448557504255-0.0335240482120.5206475871482.15854994604-1.79326611611-0.974030314969-0.2563703393471.979597499411.120558504490.872909912636-0.14553553255-0.03709536190250.9073668336140.0172601033090.515533947887-18.36103151032.27261306665-37.426345446
85.25042647396-2.032195597891.066001807095.91647724297-2.599330670175.014186193640.50499762540.643278188331-0.0968440899734-1.13248168686-0.3317927436280.03387762842750.1367025603150.401831977593-0.2256928869190.7505003362180.0700925138342-0.0477125409510.7790474830.01636593872380.49851929531-20.4288790735.0913306859-13.8825036669
94.068423361060.3115263115953.812821208923.4287204973-2.798098062816.62056816991-0.131814406155-1.18064483129-0.864709084702-0.07452707856180.7293785498471.087130133710.516648109447-0.229149355738-0.3973536435110.641118774081-0.206488917051-0.008508690254920.7391055503188.43058117233E-50.72827203227-22.854807067719.6860572722-4.33291791398
104.673679441-2.60340296137-1.947903220946.07145278876-4.001549749526.237827746030.3593436268290.218759297568-0.0361645697319-0.6577234213870.4789653812110.4192705090390.3091830935480.871512036316-1.131585583960.867791910635-0.006062155049460.01418651926341.16945100726-0.136154385060.564244748943-16.089715331515.4722062911-10.4838574102
119.48298131626-1.431396554372.034346058728.09537957717-0.5961637321985.17342077816-0.2746843500491.367974299860.634767907973-0.5094023141180.166354476382-1.115155134790.4248113138960.492411865070.1026295608580.709371398194-0.09013768810170.08516802585770.953352339990.09381879347610.586058826604-14.032412656824.0787861917-10.282521558
124.47149144217-2.990865311-0.4127788955259.081952266940.8486033300655.63159456898-0.1757287307850.03403275549920.6048040042810.5922002040920.201141789922-0.765850386569-0.7395470934590.415979351719-0.1079864524210.718820028251-0.0900526450604-0.03286708526370.6427659718120.04269013944240.481758676974-18.025786664735.70781700170.18597951298
136.049941348134.75604077708-3.556871581366.49191832164-0.5607386185195.42593545723-2.634267253072.11579386598-2.09021992204-2.473709898781.78506551779-2.73450484072-0.1096424978891.127244834930.7240440744861.19555298015-0.1239415084780.1850511876551.56541363872-0.2823676093871.2289957126-3.2515741373515.6875586211-14.8585774201
145.049896809580.7064297669170.8514708273172.63050588581-0.8816434372125.184767373950.04884841396390.105495617250.5234966005620.0974845785818-0.185700150221-0.605079834775-0.5444861437670.9075625061920.05335558282530.604184647574-0.1399468186510.01559895842580.648321808789-0.0004352785493230.493194872886-12.916067866330.6829640431-2.60343015478
153.34193624427-2.03605412306-0.6267508931477.148476605586.899977846268.16332526472-0.271804182984-0.110853340444-0.349689546306-1.29747839967-0.0297719296770.1429781802080.42140566897-0.06163391269820.3913301964941.10945133469-0.002845217205780.204641819920.8808116758250.0278945588410.65501104393-32.19684691482.66824526726-25.5145215994
163.093384887723.55770730221.249063738367.566696032765.704185025636.72203019818-0.858812090410.8750910143050.380628768547-1.555227494920.4178856904040.671754806637-0.193482338528-1.506019216320.4033993256250.935875602411-0.23368581075-0.02671484830190.890163823455-0.08142128246830.606344736826-39.557460676812.9651535267-28.9647135588
177.32310335986-3.364894983450.7105236579528.880695937-1.738832203712.555186988560.0543931499505-0.880982414794-0.6293941319870.1398367137850.018689831623-0.6501167390111.69593792602-0.00835027568901-0.0758671632911.09569090274-0.06132638513870.09751233981110.812781259698-0.01836167333140.574443788953-33.2836742868-2.96294698027-16.1101296982
183.110804159630.09784116636460.1062468313455.07852539014-2.289181548365.30710659258-0.537489581955-0.246488544445-0.205930343137-0.2791564246240.17854302955-0.5017358952860.728445008891-0.5393019625270.3076553417430.8046907776150.001684401547430.1855863073660.8835825013-0.0394729367040.464876569974-38.36971450471.7289865669-15.0074142088
196.923221249461.186154097123.57165797381.51671581334-0.03784069281965.47871877041-0.6839851593181.74151683739-0.0479623995691-2.246685269560.4728850371831.889532808751.21133454741.147484897640.4486297991011.55377237347-0.121953504018-0.3190266536211.696652175970.3563682650530.962704231845-49.242884580616.4232685582-31.7168191569
202.92562581105-4.142691737253.863532625597.70733500216-6.685963485255.887973410380.3505739727960.2178609736240.832646306925-0.655128554148-0.3847393917770.2027567649581.08893491331-1.6717236993-0.2575850183830.849865452975-0.05114486920660.04739070147161.04534453614-0.1487266360780.53072069294-40.733389530411.942909634-15.8926494548
213.67894316155-5.08669253609-0.6656595332497.753930363431.752049234921.42450965279-0.2201247185680.997396705004-1.89238503943-0.242332706944-0.1179522798250.1933033424271.93627848541-0.6068331391270.3720862955641.15331284074-0.2343363703470.2887179813650.637808802675-0.3648736195550.938887880342-36.5119341764-7.27850390249-18.6637853765
221.6337903393-1.6455449753-2.178649601722.765133955140.1850935500417.8487117847-0.9336156817150.793156890782-0.2210818556130.2857068081960.43165330008-0.9196711948010.934911670191-1.48219922770.6739360289810.795697035396-0.3329183390140.1418385453271.09697412116-0.06733184966750.68423098783-42.90059084030.75378456884-18.1993841025
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 26 through 35 )CA26 - 35
22chain 'C' and (resid 36 through 40 )CA36 - 40
33chain 'C' and (resid 41 through 44 )CA41 - 44
44chain 'D' and (resid 26 through 30 )DB26 - 30
55chain 'D' and (resid 31 through 35 )DB31 - 35
66chain 'D' and (resid 36 through 40 )DB36 - 40
77chain 'D' and (resid 41 through 44 )DB41 - 44
88chain 'A' and (resid 1 through 13 )AC1 - 131 - 13
99chain 'A' and (resid 14 through 22 )AC14 - 2214 - 22
1010chain 'A' and (resid 23 through 32 )AC23 - 3223 - 32
1111chain 'A' and (resid 33 through 49 )AC33 - 4933 - 49
1212chain 'A' and (resid 50 through 83 )AC50 - 8350 - 83
1313chain 'A' and (resid 84 through 93 )AC84 - 9384 - 93
1414chain 'A' and (resid 94 through 123 )AC94 - 12394 - 123
1515chain 'B' and (resid 1 through 22 )BH1 - 221 - 22
1616chain 'B' and (resid 23 through 41 )BH23 - 4123 - 41
1717chain 'B' and (resid 42 through 66 )BH42 - 6642 - 66
1818chain 'B' and (resid 67 through 83 )BH67 - 8367 - 83
1919chain 'B' and (resid 84 through 93 )BH84 - 9384 - 93
2020chain 'B' and (resid 94 through 101 )BH94 - 10194 - 101
2121chain 'B' and (resid 102 through 110 )BH102 - 110102 - 110
2222chain 'B' and (resid 111 through 123 )BH111 - 123111 - 123

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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