[English] 日本語
Yorodumi
- PDB-5ea7: Crystal Structure of Inhibitor BMS-433771 in Complex with Prefusi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ea7
TitleCrystal Structure of Inhibitor BMS-433771 in Complex with Prefusion RSV F Glycoprotein
ComponentsFusion glycoprotein F0
KeywordsCELL INVASION/INHIBITOR / Class I viral fusion protein / fusion / respiratory syncytial virus / prefusion / viral protein / fusion inhibitor / CELL INVASION-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Chem-5NO / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 Å
AuthorsBattles, M.B. / McLellan, J.S. / Arnoult, E. / Roymans, D. / Langedijk, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Charles H. Hood Foundation United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors.
Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / ...Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / Arnoult, E. / Peeples, M.E. / Roymans, D. / McLellan, J.S.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2838
Polymers63,2181
Non-polymers1,0657
Water43224
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,85024
Polymers189,6553
Non-polymers3,19521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16960 Å2
ΔGint-259 kcal/mol
Surface area50910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.590, 169.590, 169.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-705-

HOH

-
Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 63218.344 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: S190F, V207L, S155C, S290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Plasmid: p(alpha)H / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-5NO / 1-cyclopropyl-3-[[1-(4-oxidanylbutyl)benzimidazol-2-yl]methyl]imidazo[4,5-c]pyridin-2-one / BMS-433771


Mass: 377.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→41.13 Å / Num. obs: 20080 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.074 / Net I/σ(I): 9.1 / Num. measured all: 178444 / Scaling rejects: 62
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-39.21.66922608028500.5420.585100
9.01-41.137.70.0520.857257420.9970.01898.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MMS

4mms


Resolution: 2.851→41.13 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 979 4.89 %Random selection
Rwork0.196 19060 --
obs0.1982 20039 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.4 Å2 / Biso mean: 67.3919 Å2 / Biso min: 29.49 Å2
Refinement stepCycle: final / Resolution: 2.851→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 66 24 3466
Biso mean--121.01 51.19 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063496
X-RAY DIFFRACTIONf_angle_d0.9794731
X-RAY DIFFRACTIONf_chiral_restr0.036565
X-RAY DIFFRACTIONf_plane_restr0.004582
X-RAY DIFFRACTIONf_dihedral_angle_d15.7781275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8508-3.0010.37971530.307426492802
3.001-3.1890.28681340.255626502784
3.189-3.43510.28951360.23326782814
3.4351-3.78050.22111350.189726902825
3.7805-4.32710.21111270.180927302857
4.3271-5.44970.21021460.157327452891
5.4497-41.13590.23521480.188229183066
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)
12.1866-1.977-2.04296.84543.17462.2224-0.2248-0.1838-0.1690.61630.12990.29090.1920.23230.08330.44140.0026-0.02120.54890.06730.28852.95885.935732.4098
24.18981.14943.25370.97192.05394.44960.05260.6421-0.6691-0.26830.12810.02010.3232-0.0544-0.27910.7782-0.0038-0.04840.6202-0.17180.72865.2391-17.2988-9.9043
34.3229-0.04650.52090.94931.44564.5312-0.02220.3258-1.1339-0.36980.3169-0.04480.63210.6707-0.31470.58120.0573-0.0420.4782-0.01680.632518.9348-12.58689.0667
46.80210.6220.48145.01670.01693.03340.33840.5873-1.7039-0.1624-0.2517-0.25460.56890.0924-0.02691.1951-0.0855-0.13540.5388-0.12121.1693.7493-27.5889-3.4058
53.3742-0.59580.25990.74970.273.73390.03050.0392-0.566-0.164-0.02690.3710.4998-0.7244-0.06420.6927-0.1332-0.10980.4816-0.04680.74121.4184-14.47493.3481
66.6593-0.0347-2.06372.90940.29076.0140.29910.2209-0.320.0809-0.09470.07950.5716-0.3133-0.09520.5572-0.1166-0.19910.3482-0.00770.59396.2356-13.868310.5688
72.70890.39860.11887.91583.65553.228-0.028-0.29760.08460.0294-0.10740.4152-0.2216-0.17960.13690.3298-0.0001-0.0340.4050.02220.3358.604711.388130.5006
89.44425.02794.48196.75923.44657.5624-0.36750.04960.2126-0.18890.01710.5849-0.0712-0.08450.27760.42330.035-0.01420.4026-0.03140.50387.4451.134124.3382
94.3641-0.2931.11514.52471.71911.72210.0568-0.6895-0.01650.60140.0693-0.40650.1509-0.0795-0.11370.4650.0351-0.00750.51950.00730.34799.372417.269834.4388
108.3081-0.0343-2.28917.2591-3.21945.23380.2038-0.10510.52780.0829-0.01130.7027-0.2163-0.5426-0.23050.4890.10030.04720.448-0.09270.4458-8.515826.521729.3648
116.6572-0.67644.48143.268-0.59379.4404-0.1939-0.5869-0.16910.261-0.07690.68320.2179-0.73320.26060.40920.08460.12370.4269-0.03120.4636-7.029217.899730.2423
126.043.74830.45229.3355-0.3553.91090.4205-0.64790.82470.9191-0.6332-1.5984-0.49990.7257-0.10190.7449-0.0411-0.21850.6323-0.03940.83723.53729.1438.601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 52 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 53 through 98 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 137 through 170 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 171 through 219 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 220 through 267 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 268 through 302 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 303 through 352 )F0
8X-RAY DIFFRACTION8chain 'F' and (resid 353 through 376 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 377 through 416 )F0
10X-RAY DIFFRACTION10chain 'F' and (resid 417 through 443 )F0
11X-RAY DIFFRACTION11chain 'F' and (resid 444 through 473 )F0
12X-RAY DIFFRACTION12chain 'F' and (resid 474 through 512 )F0

+
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