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- PDB-6jyj: Crystal structure of FAM46B (TENT5B) -

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Basic information

Entry
Database: PDB / ID: 6jyj
TitleCrystal structure of FAM46B (TENT5B)
ComponentsTerminal nucleotidyltransferase 5B
KeywordsGENE REGULATION / FAM46B(TENT5B) / FAM46(TENT5) / poly(A)polymerase
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / mRNA stabilization / poly(A) RNA polymerase activity / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / early endosome membrane
Similarity search - Function
Nucleotidyltransferase / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain ...Nucleotidyltransferase / ADP-ribosylation factor-binding protein GGA3 / N-terminal extension of GAT domain / N-terminal extension of GAT domain / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / ENTH/VHS / Clathrin adaptor, appendage, Ig-like subdomain superfamily
Similarity search - Domain/homology
CITRATE ANION / Golgi-associated, gamma adaptin ear-containing, ARF-binding protein 3
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69319882982 Å
AuthorsZhang, H. / Hu, J.L. / Gao, S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells.
Authors: Hu, J.L. / Liang, H. / Zhang, H. / Yang, M.Z. / Sun, W. / Zhang, P. / Luo, L. / Feng, J.X. / Bai, H. / Liu, F. / Zhang, T. / Yang, J.Y. / Gao, Q. / Long, Y. / Ma, X.Y. / Chen, Y. / Zhong, Q. ...Authors: Hu, J.L. / Liang, H. / Zhang, H. / Yang, M.Z. / Sun, W. / Zhang, P. / Luo, L. / Feng, J.X. / Bai, H. / Liu, F. / Zhang, T. / Yang, J.Y. / Gao, Q. / Long, Y. / Ma, X.Y. / Chen, Y. / Zhong, Q. / Yu, B. / Liao, S. / Wang, Y. / Zhao, Y. / Zeng, M.S. / Cao, N. / Wang, J. / Chen, W. / Yang, H.T. / Gao, S.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal nucleotidyltransferase 5B
B: Terminal nucleotidyltransferase 5B
C: Terminal nucleotidyltransferase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5076
Polymers137,9393
Non-polymers5673
Water72140
1
A: Terminal nucleotidyltransferase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1692
Polymers45,9801
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16190 Å2
MethodPISA
2
B: Terminal nucleotidyltransferase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1692
Polymers45,9801
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint1 kcal/mol
Surface area16200 Å2
MethodPISA
3
C: Terminal nucleotidyltransferase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1692
Polymers45,9801
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.605, 76.120, 135.075
Angle α, β, γ (deg.)90.000, 96.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPRO(chain 'A' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))AA12 - 12219 - 129
12LYSLYSPHEPHE(chain 'A' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))AA129 - 195136 - 202
13ASNASNGLNGLN(chain 'A' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))AA201 - 345208 - 352
21ALAALAPROPRO(chain 'B' and (resid 12 through 122 or resid 129 through 345))BB12 - 12219 - 129
22LYSLYSPHEPHE(chain 'B' and (resid 12 through 122 or resid 129 through 345))BB129 - 195136 - 202
23ASNASNGLNGLN(chain 'B' and (resid 12 through 122 or resid 129 through 345))BB201 - 345208 - 352
31ALAALAPROPRO(chain 'C' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))CC12 - 12219 - 129
32LYSLYSPHEPHE(chain 'C' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))CC129 - 195136 - 202
33ASNASNGLNGLN(chain 'C' and (resid 12 through 122 or resid 129 through 195 or resid 201 through 345))CC201 - 345208 - 352

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Components

#1: Protein Terminal nucleotidyltransferase 5B


Mass: 45979.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: tent5b, fam46b / Production host: Escherichia coli (E. coli) / References: UniProt: F7E7M3
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2% tacsimate pH5.0, 0.15M sodium citrate tribasic dehydrate pH5.6, 10% PEG3350
PH range: 5.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.69→47.132 Å / Num. obs: 33266 / % possible obs: 99.2 % / Redundancy: 3.41 % / Biso Wilson estimate: 49.7849002172 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.12
Reflection shellResolution: 2.6932→2.7724 Å / Redundancy: 3.36 % / Num. unique obs: 3214 / Rsym value: 0.439 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAM46C

Resolution: 2.69319882982→47.1318099599 Å / SU ML: 0.431184749355 / Cross valid method: FREE R-VALUE / σ(F): 1.36979433413 / Phase error: 27.4784753528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251823896549 1683 5.06104528778 %
Rwork0.20365366353 31571 -
obs0.206061753777 33254 99.2567829747 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.2704045419 Å2
Refinement stepCycle: LAST / Resolution: 2.69319882982→47.1318099599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7988 0 39 40 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002099044586668179
X-RAY DIFFRACTIONf_angle_d0.53104712206911020
X-RAY DIFFRACTIONf_chiral_restr0.04025064666721216
X-RAY DIFFRACTIONf_plane_restr0.003154655997141422
X-RAY DIFFRACTIONf_dihedral_angle_d17.95039673185000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6932-2.77240.4111368536441620.3318629104922555X-RAY DIFFRACTION97.5933908046
2.7724-2.86190.3681695424551270.271460863852593X-RAY DIFFRACTION98.5150307859
2.8619-2.96420.3146671599131370.2433877597832617X-RAY DIFFRACTION99.3506493506
2.9642-3.08280.2808194814811210.2498140016222640X-RAY DIFFRACTION99.3522849946
3.0828-3.22310.3264193005541410.2528814325232617X-RAY DIFFRACTION99.3873873874
3.2231-3.3930.2800994286861430.2276675567132593X-RAY DIFFRACTION99.5271007639
3.393-3.60550.2726885181361430.2124646201592640X-RAY DIFFRACTION99.6776504298
3.6055-3.88380.245277350131420.1958059176412639X-RAY DIFFRACTION99.7131588383
3.8838-4.27440.2277359387321490.1747797274832642X-RAY DIFFRACTION99.6785714286
4.2744-4.89230.1940314546491410.1628515252641X-RAY DIFFRACTION99.7490139835
4.8923-6.16170.2494223517411270.1950290381362686X-RAY DIFFRACTION99.6104815864
6.1617-47.130.1986092154211500.1782770635922708X-RAY DIFFRACTION99.0297990298
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)
15.17268603044-1.44181395469-0.4084557008382.50741660636-0.6253831512963.97038967638-0.0844877331572-0.278643115888-0.01149199101240.0678109379447-0.117275470999-0.6298461330010.17558265671.277622951290.1205542614130.3434766208870.0609097527215-0.005871563460470.7326113610950.1392488414290.4422174221829.027034614119.2504173323-2.84943291039
20.681292928711-0.5301600843870.9001948618291.40370934093-1.998107010315.999384687590.124608516943-0.02638151054180.05264868379480.186499069833-0.08534851918730.0402257080534-0.2446699948530.170188667232-0.02438761107510.260187070054-0.06214705233530.02646501071240.305257850727-0.03183344148630.33495995622416.40639047316.277406866814.4280011108
33.41350773998-0.9335388170565.14014423246.61429202034-3.229849024758.15492120407-0.0499029808150.315835007542-0.6384050504090.5371342464070.2187313797760.4459002478150.494508925345-0.0040394404378-0.1795193332970.467407319477-0.07730501664120.00821744136520.305786965178-0.07169928414470.22299228546314.510331200718.474954366440.9212202508
49.7757670861-2.06256640378-2.787971644457.32322166343.86518192929.121121437330.05029884616060.08359780415360.123588040039-0.660834959196-0.08885252016221.16833612999-1.35548056302-0.59037685717-0.0510859820230.5780576939310.0827875208975-0.05753006992240.4379297448210.1028862951630.49932837198310.292247969441.114614019237.6033083455
52.153879978160.01664773260330.5578153027085.95387317204-0.7862371386643.843623496040.0223095289240.1237009621930.2960410176650.2569367579880.303052490564-0.0142142728578-0.760772841208-0.381987110106-0.4141687098130.4059643400610.0577418096369-0.01456609712990.312571407826-0.06406584972030.24882041149319.395272473330.795409915142.3104556713
65.19759159032-2.14696396383-0.9641908920937.896118196580.6252769763135.61736640773-0.06207492022090.5284807464730.914043274599-0.4720083773470.07021026639150.242188143456-1.05496362975-0.354045908248-0.2330686796590.689626664214-0.0450472263934-0.01967275817450.4148777134290.08737448651070.48025290440716.690445131649.594980628538.0436325029
72.696898178312.629145286430.3354848298797.1099860981.951569467926.33651451152-0.0614795330283-0.06019979125020.01392846249330.06200480067050.019650574505-0.0153864506077-0.557093370093-0.09649943875310.09770481111620.3685196133980.07108514105620.04237787335040.2828942737350.05793992791460.25699437806919.267097062829.824261494642.1958740276
83.05538881415-1.0661362931-0.1860045079352.435343460842.639692007823.220383738580.0549628564218-0.140309401103-0.05792534466620.3546855700420.0352299426513-0.2297891276310.4806995942810.934239085374-0.4152572063870.603862335216-0.0376010915346-0.02914259056090.3768365319580.02356372706120.35735547240625.102910843820.034520593353.3714068907
92.617532493742.832882716470.9582364620643.593039740932.435228749725.32102155549-0.07272211154420.21732491141-0.0128721087354-0.1882579850270.186730140722-0.004922148640920.0468111283944-0.0137693210214-0.09651603187280.3718753852330.02433416728410.01402421272560.2621647837440.04174622062340.28183869534123.435738979132.794230033965.2715159076
108.956252715890.2397867888170.4603394736787.118146983170.5800474681099.01111631180.000596581825597-0.01121647963390.3686102379910.03717827903140.109628444563-0.288824639645-0.432435257342-0.0750823764349-0.09832185801790.4684482733960.06201172454950.009819765636120.2134187717360.008778411676950.17521560753320.373737740635.954257698574.5222304203
115.2507646785-1.77286816484-0.206070449012.88805224209-0.3727396200433.71135310828-0.187931825189-0.40288772121-0.926431190448-0.0374822773860.1787814285550.08631138618240.8817350342620.3678268461290.02928220794380.5357603745210.04288769880540.08703916532990.3389846126660.100337952640.43072132819338.099415234758.432932837450.5067336017
123.52447557606-2.08803790964-0.6663479506256.74639140965-2.145100019853.9836011347-0.246537013377-0.33831234134-0.737178265480.0298658277873-0.0870385229697-0.5604798436470.8377563280021.039952386810.2211127612240.535060231620.1605828466290.1301780842520.638571043220.09595805647090.54411018321749.952925118557.072848054450.5572529459
135.827568158460.513648505082-1.28132191881.96057004968-0.1241049702466.39200120752-0.01075957160310.236491511372-0.2195077777130.265646215192-0.104963868803-0.397425529752-0.3533067578220.1183971402520.08660609802310.389716163375-0.0412068481488-0.06965087681450.26259171769-0.04768710081450.29032011204835.632975728270.730082880344.1649649331
142.325623232540.6715844233230.08518955828924.264476760170.3879396323865.784765222340.27948861627-0.2973992207660.6701366756470.15602260599-0.0700965785884-0.143086781584-0.8110811357830.239150689278-0.2009613451860.394140631734-0.08139477918080.03578877236090.323391313583-0.03234410379060.39245414265647.138950994274.809437163826.982254191
156.865372254821.94065312038-0.44443660084.424733325021.020651891367.365145030890.0521063851767-0.159936434781-0.5544635858030.3637404811620.078087054892-0.3673737034440.5649720783180.400862829568-0.1577622502890.3131273881870.0634448895338-0.05696460590290.255800510402-0.02521201411140.28274316924852.776899689563.191277593220.4500781419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 346 )
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 31 )
4X-RAY DIFFRACTION4chain 'B' and (resid 32 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 147 )
7X-RAY DIFFRACTION7chain 'B' and (resid 148 through 211 )
8X-RAY DIFFRACTION8chain 'B' and (resid 212 through 241 )
9X-RAY DIFFRACTION9chain 'B' and (resid 242 through 300 )
10X-RAY DIFFRACTION10chain 'B' and (resid 301 through 345 )
11X-RAY DIFFRACTION11chain 'C' and (resid 12 through 81 )
12X-RAY DIFFRACTION12chain 'C' and (resid 82 through 173 )
13X-RAY DIFFRACTION13chain 'C' and (resid 174 through 241 )
14X-RAY DIFFRACTION14chain 'C' and (resid 242 through 278 )
15X-RAY DIFFRACTION15chain 'C' and (resid 279 through 347 )

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