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- PDB-3l88: Crystal structure of the human Adenovirus type 21 fiber knob -

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Basic information

Entry
Database: PDB / ID: 3l88
TitleCrystal structure of the human Adenovirus type 21 fiber knob
ComponentsFiber proteinFibrous protein
KeywordsVIRAL PROTEIN / Adenovirus / Fiber Knob
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell
Similarity search - Function
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 21
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCupelli, K. / Jost, M. / Persson, B.D. / Stehle, T.
CitationJournal: J.Virol. / Year: 2010
Title: Structure of adenovirus type 21 knob in complex with CD46 reveals key differences in receptor contacts among species B adenoviruses.
Authors: Cupelli, K. / Muller, S. / Persson, B.D. / Jost, M. / Arnberg, N. / Stehle, T.
History
DepositionDec 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
D: Fiber protein
E: Fiber protein
F: Fiber protein
G: Fiber protein
H: Fiber protein
I: Fiber protein
J: Fiber protein
K: Fiber protein
L: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,31829
Polymers266,62612
Non-polymers69217
Water1,20767
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7946
Polymers66,6563
Non-polymers1383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-49 kcal/mol
Surface area23110 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9798
Polymers66,6563
Non-polymers3225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-51 kcal/mol
Surface area22590 Å2
MethodPISA
3
G: Fiber protein
H: Fiber protein
I: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7025
Polymers66,6563
Non-polymers462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-58 kcal/mol
Surface area23020 Å2
MethodPISA
4
J: Fiber protein
K: Fiber protein
L: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,84210
Polymers66,6563
Non-polymers1867
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-84 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.000, 63.920, 209.350
Angle α, β, γ (deg.)90.00, 91.70, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

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
11ASNASNPROPROAA132 - 14010 - 18
21ASNASNPROPROBB132 - 14010 - 18
31ASNASNPROPROCC132 - 14010 - 18
41ASNASNPROPRODD132 - 14010 - 18
51ASNASNPROPROEE132 - 14010 - 18
61ASNASNPROPROFF132 - 14010 - 18
71ASNASNPROPROGG132 - 14010 - 18
81ASNASNPROPROHH132 - 14010 - 18
91ASNASNPROPROII132 - 14010 - 18
101ASNASNPROPROJJ132 - 14010 - 18
111ASNASNPROPROKK132 - 14010 - 18
121ASNASNPROPROLL132 - 14010 - 18
12THRTHRPROPROAA150 - 24128 - 119
22THRTHRPROPROBB150 - 24128 - 119
32THRTHRPROPROCC150 - 24128 - 119
42THRTHRPROPRODD150 - 24128 - 119
52THRTHRPROPROEE150 - 24128 - 119
62THRTHRPROPROFF150 - 24128 - 119
72THRTHRPROPROGG150 - 24128 - 119
82THRTHRPROPROHH150 - 24128 - 119
92THRTHRPROPROII150 - 24128 - 119
102THRTHRPROPROJJ150 - 24128 - 119
112THRTHRPROPROKK150 - 24128 - 119
122THRTHRPROPROLL150 - 24128 - 119
13GLUGLUSERSERAA250 - 262128 - 140
23GLUGLUSERSERBB250 - 262128 - 140
33GLUGLUSERSERCC250 - 262128 - 140
43GLUGLUSERSERDD250 - 262128 - 140
53GLUGLUSERSEREE250 - 262128 - 140
63GLUGLUSERSERFF250 - 262128 - 140
73GLUGLUSERSERGG250 - 262128 - 140
83GLUGLUSERSERHH250 - 262128 - 140
93GLUGLUSERSERII250 - 262128 - 140
103GLUGLUSERSERJJ250 - 262128 - 140
113GLUGLUSERSERKK250 - 262128 - 140
123GLUGLUSERSERLL250 - 262128 - 140
14LEULEUMETMETAA267 - 275145 - 153
24LEULEUMETMETBB267 - 275145 - 153
34LEULEUMETMETCC267 - 275145 - 153
44LEULEUMETMETDD267 - 275145 - 153
54LEULEUMETMETEE267 - 275145 - 153
64LEULEUMETMETFF267 - 275145 - 153
74LEULEUMETMETGG267 - 275145 - 153
84LEULEUMETMETHH267 - 275145 - 153
94LEULEUMETMETII267 - 275145 - 153
104LEULEUMETMETJJ267 - 275145 - 153
114LEULEUMETMETKK267 - 275145 - 153
124LEULEUMETMETLL267 - 275145 - 153
15VALVALASPASPAA285 - 321163 - 199
25VALVALASPASPBB285 - 321163 - 199
35VALVALASPASPCC285 - 321163 - 199
45VALVALASPASPDD285 - 321163 - 199
55VALVALASPASPEE285 - 321163 - 199
65VALVALASPASPFF285 - 321163 - 199
75VALVALASPASPGG285 - 321163 - 199
85VALVALASPASPHH285 - 321163 - 199
95VALVALASPASPII285 - 321163 - 199
105VALVALASPASPJJ285 - 321163 - 199
115VALVALASPASPKK285 - 321163 - 199
125VALVALASPASPLL285 - 321163 - 199

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Components

#1: Protein
Fiber protein / Fibrous protein


Mass: 22218.797 Da / Num. of mol.: 12 / Fragment: Ad21 fiber knob (UNP residues 123-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 21 / Strain: 2145 / Gene: 32608, L5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q2KS96
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.45 Å / Num. all: 78468 / Num. obs: 71876 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.83
Reflection shellResolution: 2.5→2.68 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H7Z

1h7z


Resolution: 2.5→49.45 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.852 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 11.214 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25905 3593 5 %RANDOM
Rwork0.23418 ---
obs0.23543 68282 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.222 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.36 Å2
2---0.99 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17035 0 37 67 17139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02217441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5941.95623781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0352179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45525.382747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15152827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0341553
X-RAY DIFFRACTIONr_chiral_restr0.0470.22800
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.36405
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.512017
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.51016
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.3137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.374210987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.916317910
X-RAY DIFFRACTIONr_scbond_it2.81826680
X-RAY DIFFRACTIONr_scangle_it4.25935871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1130 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
5Etight positional0.10.05
6Ftight positional0.030.05
7Gtight positional0.030.05
8Htight positional0.030.05
9Itight positional0.030.05
10Jtight positional0.030.05
11Ktight positional0.030.05
12Ltight positional0.030.05
1Atight thermal0.080.5
2Btight thermal0.080.5
3Ctight thermal0.080.5
4Dtight thermal0.070.5
5Etight thermal0.080.5
6Ftight thermal0.080.5
7Gtight thermal0.080.5
8Htight thermal0.080.5
9Itight thermal0.080.5
10Jtight thermal0.070.5
11Ktight thermal0.080.5
12Ltight thermal0.080.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 230 -
Rwork0.298 4377 -
obs--79.68 %

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