[English] 日本語
Yorodumi
- PDB-1v1h: Adenovirus fibre shaft sequence N-terminally fused to the bacteri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v1h
TitleAdenovirus fibre shaft sequence N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif with a short linker
ComponentsFIBRITIN, FIBER PROTEIN
KeywordsADENOVIRUS / CHIMERA / FIBER PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #10 / reovirus attachment protein sigma1; domain 1 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...Wheat Germ Agglutinin (Isolectin 2); domain 1 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #10 / reovirus attachment protein sigma1; domain 1 / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Fibritin C-terminal / Fibritin C-terminal region / Other non-globular / Laminin / Special / Ribbon / Mainly Beta
Similarity search - Domain/homology
Fiber protein / Fibritin
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS TYPE 2
BACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPapanikolopoulou, K. / Teixeira, S. / Belrhali, H. / Forsyth, V.T. / Mitraki, A. / van Raaij, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Adenovirus Fibre Shaft Sequences Fold Into the Native Triple Beta-Spiral Fold When N-Terminally Fused to the Bacteriophage T4 Fibritin Foldon Trimerisation Motif
Authors: Papanikolopoulou, K. / Teixeira, S. / Belrhali, H. / Forsyth, V.T. / Mitraki, A. / van Raaij, M.J.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Formation of Highly Stable Chimeric Trimers by Fusion of an Adenovirus Fiber Shaft Fragment with the Foldon Domain of Bacteriophage T4 Fibritin
Authors: Papanikolopoulou, K. / Forge, V. / Goeltz, P. / Mitraki, A.
#2: Journal: Nature / Year: 1999
Title: A Triple Beta-Spiral in the Adenovirus Fibre Shaft Reveals a New Structural Motif for a Fibrous Protein
Authors: van Raaij, M.J. / Mitraki, A. / Lavigne, G. / Cusack, S.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of Bacteriophage T4 Fibritin M: A Troublesome Packing Arrangement
Authors: Strelkov, S. / Tao, Y. / Shneider, M.M. / Mesyanzhinov, V. / Rossmann, M.G.
History
DepositionApr 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBRITIN, FIBER PROTEIN
B: FIBRITIN, FIBER PROTEIN
C: FIBRITIN, FIBER PROTEIN
D: FIBRITIN, FIBER PROTEIN
E: FIBRITIN, FIBER PROTEIN
F: FIBRITIN, FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)64,7586
Polymers64,7586
Non-polymers00
Water7,963442
1
A: FIBRITIN, FIBER PROTEIN
B: FIBRITIN, FIBER PROTEIN
C: FIBRITIN, FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3793
Polymers32,3793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: FIBRITIN, FIBER PROTEIN
E: FIBRITIN, FIBER PROTEIN
F: FIBRITIN, FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3793
Polymers32,3793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.770, 183.330, 58.970
Angle α, β, γ (deg.)90.00, 129.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2019-

HOH

21B-2040-

HOH

31D-2022-

HOH

41E-2028-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.40476, -0.4564, -0.79238), (-0.223, 0.88964, -0.39851), (0.88681, 0.01541, -0.46187)66.96565, 15.85284, -4.13093
2given(-0.41406, -0.45262, -0.78974), (-0.22617, 0.89156, -0.39239), (0.88171, 0.01615, -0.47152)67.33018, 16.00517, -3.7847
3given(-0.91828, -0.06488, 0.39058), (0.2331, -0.88599, 0.40086), (0.32005, 0.45915, 0.82871)45.43064, -16.26194, -28.03097
4given(-0.47791, 0.08491, 0.8743), (-0.36738, 0.88476, -0.28674), (-0.79789, -0.45824, -0.39165)28.54939, 7.06268, 15.14585
5given(-0.48757, 0.08563, 0.86888), (-0.3617, 0.88595, -0.29028), (-0.79464, -0.4558, -0.40099)28.79466, 6.84886, 15.01443
6given(0.72944, 0.45562, 0.51023), (0.36067, -0.88996, 0.27908), (0.58124, -0.01955, -0.8135)22.7223, -6.82744, 8.05489
7given(-0.43042, -0.22665, 0.87371), (-0.4561, 0.88991, 0.00616), (-0.77892, -0.39585, -0.48641)35.60816, 16.61239, 57.44727
8given(0.73979, 0.36417, 0.56576), (0.45712, -0.88904, -0.02548), (0.49371, 0.27747, -0.82417)-18.90883, -16.25296, -2.23152
9given(0.73883, 0.35732, 0.57135), (0.45174, -0.89176, -0.02646), (0.50005, 0.27765, -0.82028)-19.04541, -15.97488, -2.65665
10given(-0.49135, -0.36474, -0.79091), (0.0777, 0.88611, -0.45691), (0.86749, -0.28596, -0.40705)28.62491, -1.58277, -16.97547
11given(-0.92714, 0.23133, 0.29478), (-0.07461, -0.8849, 0.45977), (0.36721, 0.40428, 0.83768)54.54449, 1.64928, 12.4659
12given(-0.92041, 0.23773, 0.31036), (-0.07417, -0.88564, 0.45841), (0.38385, 0.39891, 0.83279)54.49028, 1.52241, 12.2077
13given(0.12012, -0.00451, -0.99275), (-0.00864, -0.99996, 0.0035), (-0.99272, 0.00816, -0.12015)34.11697, 0.35063, 38.60129
14given(0.11649, -0.00733, -0.99316), (-0.0088, -0.99994, 0.00635), (-0.99315, 0.008, -0.11655)34.26817, 0.25672, 38.54223
15given(0.11213, -0.00884, -0.99365), (-0.01108, -0.99991, 0.00764), (-0.99363, 0.01015, -0.11222)34.42091, 0.33496, 38.47535
16given(-0.5089, 0.13598, -0.85002), (0.00606, 0.98799, 0.15442), (0.86081, 0.07343, -0.50361)60.51682, -2.32476, -3.60397
17given(-0.46237, 0.1503, -0.87386), (0.01051, 0.98639, 0.16409), (0.88663, 0.06668, -0.45765)59.03748, -3.01978, -5.15919
18given(-0.87168, -0.04331, 0.48816), (0.03503, -0.99905, -0.02607), (0.48882, -0.00562, 0.87237)40.63412, -1.10671, -26.07614
19given(-0.4804, 0.15227, 0.86373), (0.00362, 0.98515, -0.17166), (-0.87704, -0.07933, -0.47382)28.66281, 0.46336, 22.30543
20given(-0.49933, 0.15704, 0.85206), (-0.00316, 0.9831, -0.18304), (-0.8664, -0.09409, -0.4904)29.23914, 0.62156, 21.39228
21given(0.83666, -0.04839, 0.54558), (-0.13759, -0.98272, 0.12383), (0.53016, -0.17867, -0.82886)12.44819, 2.2893, 6.33045
22given(-0.51502, 0.02081, 0.85692), (0.14183, 0.98799, 0.06125), (-0.84536, 0.15308, -0.51179)33.82808, -5.27641, 49.98179
23given(0.83635, -0.14032, 0.52993), (-0.04956, -0.98208, -0.18183), (0.54594, 0.12581, -0.82832)-13.24597, 4.09547, -1.63132
24given(0.84602, -0.13569, 0.51559), (-0.05259, -0.9836, -0.17255), (0.53054, 0.11887, -0.83928)-13.5643, 3.99161, -0.86782
25given(-0.50646, 0.01233, -0.86217), (0.16695, 0.98238, -0.08403), (0.84594, -0.1865, -0.4996)34.0451, -3.12326, -14.45142
26given(-0.89103, 0.03396, 0.45267), (-0.0379, -0.99928, 0.00035), (0.45235, -0.01684, 0.89168)48.62573, 0.34033, 3.90906
27given(-0.89514, 0.04209, 0.44379), (-0.04843, -0.99882, -0.00294), (0.44314, -0.02412, 0.89613)49.08134, 0.97874, 4.07842
28given(0.02982, 0.01408, -0.99946), (-0.13762, -0.99032, -0.01805), (-0.99004, 0.13808, -0.02759)35.77655, 4.04892, 34.08782
29given(0.06436, 0.02698, -0.99756), (-0.13893, -0.98966, -0.03573), (-0.98821, 0.14089, -0.05994)34.1637, 4.73096, 34.42914
30given(0.02245, 0.01481, -0.99964), (-0.1507, -0.98842, -0.01803), (-0.98832, 0.15105, -0.01996)35.85344, 4.72923, 33.23837

-
Components

#1: Protein
FIBRITIN, FIBER PROTEIN / ARTIFICAL FUSION OF ADENOVIRUS FIBRE SHAFT WITH BACTERIOPHAGE T4 FIBRITIN FOLDON / WHISKER ANTIGEN ...ARTIFICAL FUSION OF ADENOVIRUS FIBRE SHAFT WITH BACTERIOPHAGE T4 FIBRITIN FOLDON / WHISKER ANTIGEN CONTROL PROTEIN / COLLAR PROTEIN


Mass: 10792.961 Da / Num. of mol.: 6
Fragment: SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Source method: isolated from a genetically manipulated source
Details: ARTIFICIAL FUSION PROTEIN OF ADENOVIRUS TYPE 2 FIBRE SHAFT RESIDUES 319-392 - BACTERIOPHAGE T4 FIBRITIN FOLDON RESIDUES 457-483 WITH A GLY-SER LINKER IN BETWEEN
Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 2, (gene. exp.) BACTERIOPHAGE T4 (virus)
Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P03275, UniProt: P10104
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Compound detailsADENOVIRUS FIBRE IS RESPONSIBLE FOR ADENOVIRUS RECEPTOR BINDING AND CONTAINS A VIRUS-BINDING N- ...ADENOVIRUS FIBRE IS RESPONSIBLE FOR ADENOVIRUS RECEPTOR BINDING AND CONTAINS A VIRUS-BINDING N-TERMINAL DOMAIN, A MIDDLE SHAFT DOMAIN AND A C-TERMINAL RECEPTOR-BINDING DOMAIN, BINDING TO THE HUMAN COXSACKIEVIRUS AND ADENOVIRUS PROTEIN. THE FIBRITIN CHAPERONE IS RESPONSIBLE FOR ATTACHMENT OF LONG TAIL FIBRES TO VIRUS PARTICLE. DURING PHAGE ASSEMBLY, 6 FIBRITIN MOLECULES ATTACH TO EACH VIRION NECK THROUGH THEIR N-TERMINAL DOMAINS, TO FORM A COLLAR WITH SIX FIBERS ('WHISKERS'). MOLECULES ATTACH TO EACH VIRION NECK THROUGH THEIR N-TERMINAL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.5 %
Crystal growpH: 6 / Details: 0.2 M IMIDAZOLE-MALATE PH 6.0 8% (W/V) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 44492 / % possible obs: 89 % / Redundancy: 5.8 % / Biso Wilson estimate: 22.083 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4 / Rsym value: 0.168 / % possible all: 53.9

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIU

1qiu


Resolution: 1.9→20 Å / SU B: 3.6237 / SU ML: 0.1056 / Cross valid method: THROUGHOUT / ESU R: 0.1656 / ESU R Free: 0.1584
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1624 3.7 %THIN SHELLS OF RESOLUTION
Rwork0.182 ---
obs-42866 89 %-
Displacement parametersBiso mean: 38.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.42 Å2
2---1.14 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 0 442 4962

+
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://pdbjlvh1.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