[English] 日本語
Yorodumi
- PDB-7nfr: Fujian capmidlink domain in complex with Nb8194 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nfr
TitleFujian capmidlink domain in complex with Nb8194
Components
  • NB8194
  • Polymerase basic protein 2
KeywordsVIRAL PROTEIN / Influenza polymerase / cap-binding domain / nanobody
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / : / Influenza RNA polymerase PB2 helical domain / Influenza RNA polymerase PB2 CAP binding domain
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKeown, J.R. / Grimes, J.M. / Fodor, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies.
Authors: Jeremy R Keown / Zihan Zhu / Loïc Carrique / Haitian Fan / Alexander P Walker / Itziar Serna Martin / Els Pardon / Jan Steyaert / Ervin Fodor / Jonathan M Grimes /
Abstract: Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA- ...Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA-dependent RNA polymerase which transcribes and replicates the viral RNA genome. The polymerase undergoes conformational rearrangements and interacts with viral and host proteins to perform these functions. Here we determine the structure of the 1918 influenza virus polymerase in transcriptase and replicase conformations using cryo-electron microscopy (cryo-EM). We then structurally and functionally characterise the binding of single-domain nanobodies to the polymerase of the 1918 pandemic influenza virus. Combining these functional and structural data we identify five sites on the polymerase which are sensitive to inhibition by nanobodies. We propose that the binding of nanobodies at these sites either prevents the polymerase from assuming particular functional conformations or interactions with viral or host factors. The polymerase is highly conserved across the influenza A subtypes, suggesting these sites as effective targets for potential influenza antiviral development.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase basic protein 2
B: NB8194
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8987
Polymers48,4302
Non-polymers4685
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-32 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.596, 65.462, 59.990
Angle α, β, γ (deg.)90.000, 108.216, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 34249.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/duck/Fujian/13/2002(H5N1))
Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6E3N3
#2: Antibody NB8194


Mass: 14180.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% w/v Peg3350, 0.2 M (NH4)2SO4, and 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.88→56.98 Å / Num. obs: 30100 / % possible obs: 89.92 % / Redundancy: 2 % / Biso Wilson estimate: 40.79 Å2 / CC1/2: 1 / Net I/σ(I): 9.29
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 1775 / CC1/2: 0.159

-
Processing

Software
NameVersionClassification
PHENIX1.18rc2_3794refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S5V

6s5v


Resolution: 1.88→56.98 Å / SU ML: 0.2911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 1516 5.07 %
Rwork0.1948 28372 -
obs0.1974 29888 89.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.92 Å2
Refinement stepCycle: LAST / Resolution: 1.88→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 28 77 3230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473214
X-RAY DIFFRACTIONf_angle_d0.57184334
X-RAY DIFFRACTIONf_chiral_restr0.0466485
X-RAY DIFFRACTIONf_plane_restr0.0032562
X-RAY DIFFRACTIONf_dihedral_angle_d18.2463449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.4412740.37321340X-RAY DIFFRACTION46.91
1.94-2.010.3627840.35251887X-RAY DIFFRACTION65.68
2.01-2.090.40571360.32552280X-RAY DIFFRACTION80.99
2.09-2.190.33511550.28432732X-RAY DIFFRACTION95.5
2.19-2.30.32981740.24922837X-RAY DIFFRACTION99.93
2.3-2.450.28841470.23672842X-RAY DIFFRACTION99.93
2.45-2.640.27361510.21242871X-RAY DIFFRACTION99.9
2.64-2.90.27531470.20152853X-RAY DIFFRACTION99.97
2.9-3.320.2641420.19732901X-RAY DIFFRACTION99.97
3.32-4.190.22481360.1672904X-RAY DIFFRACTION100
4.19-56.980.19461700.16332925X-RAY DIFFRACTION99.84
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)
16.18463077081-2.73366466127-1.70050777695.528941372521.289800747362.310026782190.2133098898640.576764987671-0.0853064166357-0.6046175400160.0558859141453-0.49919470472-0.1366243688631.33041974293-0.2366148176010.309736163025-0.005134003988810.0825172272410.463254871206-0.04158727358720.436440160573-9.93832859831-0.855374866665-11.4647528188
24.154519547390.5960386396650.2792016982486.42437557329-0.0002151880996069.211124577630.1144578762350.2356314319940.489941660317-0.0968265311682-0.145248516036-0.254037050343-0.689891546466-0.04345471338750.05225535866940.2455485946140.0170163479540.04340013704420.309439499501-0.03575420496190.292018255064-16.70774229464.97700896978-11.0655352713
3-0.171152082724-0.237145866532-0.3257613899673.38455116216-1.11353174191.151378917520.1093802724690.01436325775840.0882327710025-0.365346998792-0.01432883852680.01014180761090.153385430726-0.146049595703-0.07161020219880.354346968663-0.0199390058571-0.04526692380580.467333005306-0.03582932737820.362660131508-21.5096006495-10.5507418818-6.44876089648
45.940566954190.1211882683525.626645453162.05518485034-0.4792403909575.17062157715-0.255859807219-0.008594779734220.3654251763790.281328344540.02644103261590.120440295427-0.439311348418-0.09904415813850.2605079872410.35671686061-0.02890048758470.0551475743490.4631846544-0.02184797903880.398015006578-20.1289300799-20.1663505514.2942159414
57.840386854511.10794029318-4.041876659232.75681105033-1.15220222954.660260236030.05291677630520.297297635259-0.0115371347213-0.290278977189-0.1025563366420.07558856560870.1027223660790.02319752640160.03842839839740.3353128908370.00325298832194-0.0305156480960.3027419222420.003043424392140.259704437484-15.1695303307-25.9164343744-3.51590893546
61.488475992210.188295483575-0.3280130074544.972971266560.1879411730213.60717926698-0.025759722313-0.116146792026-0.1445066275490.115945871043-0.0303136742861-0.2987951035790.3905486289610.3969078973850.04537429468560.287715606020.01953159174130.02599197733230.4528541102120.03039580827810.287655493848-8.72055704586-26.99032672373.06498343129
77.9941085182-2.86090388525-2.335428018796.664255516562.538138931596.32544955559-0.327814370197-0.1520656271080.2873786619180.1937058003070.1645329220310.8897692781360.454148175875-0.3772341566110.2957760393190.366525042553-0.04957297956680.01855619776930.332635748790.09625691887270.268818569538-24.2065482951-7.20835173733-3.29583177894
86.04859652492.21126207487-3.068720579723.93457586371-3.741633699494.49952545317-0.2249726898340.3423449591-0.2107073790670.3105381871320.097913192841-0.688757451606-0.01122079341220.3873387279310.3883724035410.359430221536-0.03550184006870.04201904689860.51180080426-0.08961158848770.448104858169-11.3781482832-3.67017550847-7.73645911011
95.991969695665.294145481860.1704993230884.75325654012-1.189648303375.903246840920.218718885371-0.21013523103-0.334795022351-0.474497615262-0.555729912212-0.792748597030.2698065616820.7833793173130.3210884903840.4986467409620.09791636826960.02735052498030.521720817982-0.01115868677990.26879394904113.8898241792-24.9583720799-22.3522602051
101.95196459977-0.3800087281662.095397853756.589346239151.547648873834.365609842110.1157972762070.100931059114-0.36022073636-0.5588428033590.1711525473360.00939589840470.5651309396850.0967295175747-0.1609269264730.590515390797-0.03311359815460.03570495979350.3880209199120.002794371204920.3033004081914.28000285828-32.4063314355-27.2287279898
117.703944806413.68294828177.17276211623.237853577872.87082202469.443690686450.252661790184-0.499531887918-0.3173661093440.343636133157-0.171779718407-0.273122385668-0.209595375142-0.7032775160470.003647233608840.4875026688920.0216827888829-0.01915522811030.3822855200350.0651736214670.2776285261035.97930479228-23.5001764336-13.6755469446
129.00888323957-0.8454503008881.88046864232.435708694960.5842494835425.43052910440.5737806562020.331873799450.452804298215-0.223441288859-0.3978512219030.7400972444110.271100672291-1.310639629560.002122551841270.4676177211210.02131644410220.01098669833110.4104608997850.08736403447430.393214404623-3.39252976443-23.9952056335-25.3276138638
133.924129681572.751466515223.173966246684.095883481835.231889583318.17118852671-0.4144004619730.2065161470570.393054655563-0.729212044770.1968668193750.496413591568-0.958517636457-0.1912493920290.1562929929620.650285210880.06386315184120.04290858205760.3423318392330.0759906632540.3510637623911.79659573416-18.2671651076-25.4250141982
144.590723998672.175607910171.466570319538.28629167031-2.381547379316.110270037470.01042497026110.1878748464790.205464294589-0.214898656403-0.3437838749780.166624126719-0.03206277495380.06991422708820.2866940918850.2585489848020.0319980459990.01497255958460.3116352626880.02410956747280.2146433564737.9113935055-22.7812673721-23.4464674782
156.354704710423.346026739-1.123738211588.12242965827-2.942865413558.40401702632-0.488931530667-0.577925734573-0.3885468214210.06166938788530.6401182384160.5294712637560.496984366431-0.380563471393-0.002855497531650.5412343327950.08288937045990.0393860031720.4169257405410.02832919302450.2879227330881.27786172307-32.2128612372-15.8721515535
166.7294506364.90139734167.192476876333.938263441615.906058458319.20119034515-1.063644636650.49264775516-0.01449580151580.05817887666430.974572995011-2.29879710515-0.5102840763240.7966844359110.1004981226840.421235400647-0.0523075820624-0.1385156182940.5210374330650.01727485457650.70956664254919.6247924699-14.3109175995-16.8703910234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 252 through 272 )AA252 - 2721 - 21
22chain 'A' and (resid 273 through 305 )AA273 - 30522 - 54
33chain 'A' and (resid 306 through 335 )AA306 - 33555 - 84
44chain 'A' and (resid 336 through 358 )AA336 - 35885 - 107
55chain 'A' and (resid 359 through 405 )AA359 - 405108 - 154
66chain 'A' and (resid 406 through 485 )AA406 - 485155 - 237
77chain 'A' and (resid 486 through 507 )AA486 - 507238 - 257
88chain 'A' and (resid 508 through 532 )AA508 - 532258 - 282
99chain 'B' and (resid 1 through 17 )BF1 - 171 - 17
1010chain 'B' and (resid 18 through 33 )BF18 - 3318 - 33
1111chain 'B' and (resid 34 through 45 )BF34 - 4534 - 46
1212chain 'B' and (resid 46 through 60 )BF46 - 6047 - 61
1313chain 'B' and (resid 61 through 73 )BF61 - 7362 - 74
1414chain 'B' and (resid 74 through 98 )BF74 - 9875 - 99
1515chain 'B' and (resid 99 through 110 )BF99 - 110100 - 111
1616chain 'B' and (resid 111 through 120 )BF111 - 120112 - 121

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more