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- PDB-2iun: Structure of the C-terminal head domain of the avian adenovirus C... -

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Basic information

Entry
Database: PDB / ID: 2iun
TitleStructure of the C-terminal head domain of the avian adenovirus CELO long fibre (P21 crystal form)
ComponentsAVIAN ADENOVIRUS CELO LONG FIBRE
KeywordsVIRAL PROTEIN / RECEPTOR-BINDING / AVIAN ADENOVIRUS / TRIMERIC PROTEINS / VIRAL FIBRES / BETA-SANDWICH / FIBER PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / viral capsid / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Attachment protein shaft domain superfamily ...Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Attachment protein shaft domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fiber protein 1 / Long fiber
Similarity search - Component
Biological speciesAVIAN ADENOVIRUS GAL1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J.
Citation
Journal: J. Gen. Virol. / Year: 2007
Title: Structure of the C-terminal head domain of the fowl adenovirus type 1 long fiber.
Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Langlois, P. / van Raaij, M.J.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2006
Title: Crystallization of the C-Terminal Head Domain of the Avian Adenovirus Celo Long Fibre
Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Langlois, P. / van Raaij, M.J.
#2: Journal: J.Virol. / Year: 1996
Title: The Complete DNA Sequence and Genomic Organization of the Avian Adenovirus Celo.
Authors: Chiocca, S. / Kurzbauer, R. / Schaffner, G. / Baker, A. / Mautner, V. / Cotten, M.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: The Avian Adenovirus Penton: Two Fibres and One Base.
Authors: Hess, M. / Cuzange, A. / Ruigrok, R.W. / Chroboczek, J. / Jacrot, B.
History
DepositionJun 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Dec 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVIAN ADENOVIRUS CELO LONG FIBRE
B: AVIAN ADENOVIRUS CELO LONG FIBRE
C: AVIAN ADENOVIRUS CELO LONG FIBRE
D: AVIAN ADENOVIRUS CELO LONG FIBRE
E: AVIAN ADENOVIRUS CELO LONG FIBRE
F: AVIAN ADENOVIRUS CELO LONG FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,9607
Polymers158,9206
Non-polymers401
Water2,018112
1
A: AVIAN ADENOVIRUS CELO LONG FIBRE
B: AVIAN ADENOVIRUS CELO LONG FIBRE
C: AVIAN ADENOVIRUS CELO LONG FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5004
Polymers79,4603
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-42.2 kcal/mol
Surface area28650 Å2
MethodPQS
2
D: AVIAN ADENOVIRUS CELO LONG FIBRE
E: AVIAN ADENOVIRUS CELO LONG FIBRE
F: AVIAN ADENOVIRUS CELO LONG FIBRE


Theoretical massNumber of molelcules
Total (without water)79,4603
Polymers79,4603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-47.8 kcal/mol
Surface area28880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)55.960, 107.864, 114.833
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILEAA583 - 60038 - 55
21PROPROILEILEBB583 - 60038 - 55
31PROPROILEILECC583 - 60038 - 55
41PROPROILEILEDD583 - 60038 - 55
51PROPROILEILEEE583 - 60038 - 55
61PROPROILEILEFF583 - 60038 - 55
12ALAALAALAALAAA609 - 63564 - 90
22ALAALAALAALABB609 - 63564 - 90
32ALAALAALAALACC609 - 63564 - 90
42ALAALAALAALADD609 - 63564 - 90
52ALAALAALAALAEE609 - 63564 - 90
62ALAALAALAALAFF609 - 63564 - 90
13GLYGLYSERSERAA642 - 66897 - 123
23GLYGLYSERSERBB642 - 66897 - 123
33GLYGLYSERSERCC642 - 66897 - 123
43GLYGLYSERSERDD642 - 66897 - 123
53GLYGLYSERSEREE642 - 66897 - 123
63GLYGLYSERSERFF642 - 66897 - 123
14VALVALSERSERAA675 - 692130 - 147
24VALVALSERSERBB675 - 692130 - 147
34VALVALSERSERCC675 - 692130 - 147
44VALVALSERSERDD675 - 692130 - 147
54VALVALSERSEREE675 - 692130 - 147
64VALVALSERSERFF675 - 692130 - 147
15THRTHRPROPROAA695 - 700150 - 155
25THRTHRPROPROBB695 - 700150 - 155
35THRTHRPROPROCC695 - 700150 - 155
45THRTHRPROPRODD695 - 700150 - 155
55THRTHRPROPROEE695 - 700150 - 155
65THRTHRPROPROFF695 - 700150 - 155
16TRPTRPSERSERAA706 - 711161 - 166
26TRPTRPSERSERBB706 - 711161 - 166
36TRPTRPSERSERCC706 - 711161 - 166
46TRPTRPSERSERDD706 - 711161 - 166
56TRPTRPSERSEREE706 - 711161 - 166
66TRPTRPSERSERFF706 - 711161 - 166
17LEULEUILEILEAA713 - 719168 - 174
27LEULEUILEILEBB713 - 719168 - 174
37LEULEUILEILECC713 - 719168 - 174
47LEULEUILEILEDD713 - 719168 - 174
57LEULEUILEILEEE713 - 719168 - 174
67LEULEUILEILEFF713 - 719168 - 174
18PHEPHESERSERAA721 - 726176 - 181
28PHEPHESERSERBB721 - 726176 - 181
38PHEPHESERSERCC721 - 726176 - 181
48PHEPHESERSERDD721 - 726176 - 181
58PHEPHESERSEREE721 - 726176 - 181
68PHEPHESERSERFF721 - 726176 - 181
19LEULEUALAALAAA731 - 741186 - 196
29LEULEUALAALABB731 - 741186 - 196
39LEULEUALAALACC731 - 741186 - 196
49LEULEUALAALADD731 - 741186 - 196
59LEULEUALAALAEE731 - 741186 - 196
69LEULEUALAALAFF731 - 741186 - 196
110SERSERTHRTHRAA743 - 748198 - 203
210SERSERTHRTHRBB743 - 748198 - 203
310SERSERTHRTHRCC743 - 748198 - 203
410SERSERTHRTHRDD743 - 748198 - 203
510SERSERTHRTHREE743 - 748198 - 203
610SERSERTHRTHRFF743 - 748198 - 203
111TYRTYRGLYGLYAA750 - 765205 - 220
211TYRTYRGLYGLYBB750 - 765205 - 220
311TYRTYRGLYGLYCC750 - 765205 - 220
411TYRTYRGLYGLYDD750 - 765205 - 220
511TYRTYRGLYGLYEE750 - 765205 - 220
611TYRTYRGLYGLYFF750 - 765205 - 220
112ASNASNPROPROAA767 - 771222 - 226
212ASNASNPROPROBB767 - 771222 - 226
312ASNASNPROPROCC767 - 771222 - 226
412ASNASNPROPRODD767 - 771222 - 226
512ASNASNPROPROEE767 - 771222 - 226
612ASNASNPROPROFF767 - 771222 - 226
113ALAALAGLNGLNAA773 - 793228 - 248
213ALAALAGLNGLNBB773 - 793228 - 248
313ALAALAGLNGLNCC773 - 793228 - 248
413ALAALAGLNGLNDD773 - 793228 - 248
513ALAALAGLNGLNEE773 - 793228 - 248
613ALAALAGLNGLNFF773 - 793228 - 248

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Components

#1: Protein
AVIAN ADENOVIRUS CELO LONG FIBRE


Mass: 26486.662 Da / Num. of mol.: 6 / Fragment: C-TERMINAL HEAD DOMAIN, RESIDUES 579-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN ADENOVIRUS GAL1 / Strain: TYPE 1 / Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q64787, UniProt: Q64761*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLISED SEQUENCE CONTAINS N-TERMINAL PURIFICATION TAG (ENCODED BY THE EXPRESSION PLASMID PET28C+)

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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growpH: 8.5
Details: 2.0 M AMMONIUMDIHYDROGENPHOSPHATE; 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: BRUKER-NONIUS / Detector: CCD / Date: May 19, 2006 / Details: OSMIC CONFOCAL MIRRORS (MULTI-LAYER)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→49.6 Å / Num. obs: 33536 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IUM

2ium


Resolution: 2.8→28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.542 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1554 4.6 %SHELLS
Rwork0.153 ---
obs0.155 31934 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.53 Å2
2--1.12 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9594 0 1 112 9707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9613542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44751260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68224.677372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.953151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6981518
X-RAY DIFFRACTIONr_chiral_restr0.090.21554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027554
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.23741
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.26916
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.18626395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.173310290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14933948
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.53853252
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1305 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
5Etight positional0.050.05
6Ftight positional0.050.05
1Atight thermal0.421
2Btight thermal0.361
3Ctight thermal0.431
4Dtight thermal0.381
5Etight thermal0.411
6Ftight thermal0.41
LS refinement shellResolution: 2.8→2.99 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.23 263
Rwork0.195 5613

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