[English] 日本語
Yorodumi
- PDB-1aym: HUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aym
TitleHUMAN RHINOVIRUS 16 COAT PROTEIN AT HIGH RESOLUTION
Components(HUMAN RHINOVIRUS 16 COAT ...) x 4
KeywordsVIRUS / HUMAN RHINOVIRUS 16 / RNA / SITE-DIRECTED MUTAGENESIS / RHINOVIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / MYRISTIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR / Resolution: 2.15 Å
AuthorsHadfield, A.T. / Rossmann, M.G.
Citation
Journal: Structure / Year: 1997
Title: The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.
Authors: Hadfield, A.T. / Lee, W. / Zhao, R. / Oliveira, M.A. / Minor, I. / Rueckert, R.R. / Rossmann, M.G.
#1: Journal: Structure / Year: 1993
Title: The Structure of Human Rhinovirus 16
Authors: Oliveira, M.A. / Zhao, R. / Lee, W.M. / Kremer, M.J. / Minor, I. / Rueckert, R.R. / Diana, G.D. / Pevear, D.C. / Dutko, F.J. / Mckinlay, M.A. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A
Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / Mckinlay, M.A. / Pevear, D.C.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structure of a Human Rhinovirus Complexed with its Receptor Molecule
Authors: Olson, N.H. / Kolatkar, P.R. / Oliveira, M.A. / Cheng, R.H. / Greve, J.M. / Mcclelland, A. / Baker, T.S. / Rossmann, M.G.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
Authors: Kim, S.S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A.
#5: Journal: Trends Biochem.Sci. / Year: 1987
Title: Common Cold Viruses
Authors: Rossmann, M.G. / Arnold, E. / Griffith, J.P. / Kamer, G. / Luo, M. / Smith, T.J. / Vriend, G. / Rueckert, R.R. / Sherry, B. / Mckinlay, M.A. / Diana, G. / Otto, M.
#6: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#7: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionNov 6, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms / struct_conn
Item: _pdbx_database_status.process_site
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6747
Polymers95,1804
Non-polymers4943
Water9,602533
1
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,740,457420
Polymers5,710,811240
Non-polymers29,646180
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 478 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)478,37135
Polymers475,90120
Non-polymers2,47015
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 574 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)574,04642
Polymers571,08124
Non-polymers2,96518
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: HUMAN RHINOVIRUS 16 COAT PROTEIN
2: HUMAN RHINOVIRUS 16 COAT PROTEIN
3: HUMAN RHINOVIRUS 16 COAT PROTEIN
4: HUMAN RHINOVIRUS 16 COAT PROTEIN
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.87 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,870,228210
Polymers2,855,405120
Non-polymers14,82390
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)362.600, 347.100, 334.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, 0.25544312, 0.8274955), (0.3612676, 0.80687821, -0.46736845), (-0.78707414, 0.53263155, 0.31115577)45.3227, -32.74724, 71.34464
3generate(-0.30901699, 0.77458326, 0.5518417), (0.83998638, 0.49440059, -0.22358649), (-0.44601722, 0.39444749, -0.80341758)118.65636, -76.14089, 40.4294
4generate(-0.30901699, 0.83998639, -0.44601722), (0.77458326, 0.49440059, 0.39444749), (0.5518417, -0.22358649, -0.80341758)118.65636, -70.2124, -50.02191
5generate(0.5, 0.36126761, -0.78707414), (0.25544312, 0.80687821, 0.53263155), (0.8274955, -0.46736846, 0.31115577)45.3227, -23.15474, -75.00865
6generate(-0.80901699, 0.51914014, -0.27565379), (0.51914014, 0.41115427, -0.74929678), (-0.2756538, -0.74929679, -0.60213728)163.97905, -47.05766, 24.98675
7generate(0.06540313, -0.99785892), (0.99785892, 0.0652631, 0.00427757), (0.06540313, -0.99572244, -0.0652631)90.64539, -90.45131, -5.92849
8generate(0.80901699, -0.47871879, -0.34105692), (0.51914014, 0.30983393, 0.79655284), (-0.2756538, -0.82148114, 0.49918305)17.31173, -47.05766, 24.98675
9generate(0.5, -0.36126761, 0.78707414), (-0.25544312, 0.80687821, 0.53263155), (-0.8274955, -0.46736846, 0.31115577)45.3227, 23.15474, 75.00865
10generate(-0.5, 0.25544312, 0.8274955), (-0.25544312, 0.86949762, -0.42275607), (-0.8274955, -0.42275607, -0.36949762)135.96809, 23.15474, 75.00865
11generate(0.30901699, -0.77458326, -0.5518417), (-0.77458326, -0.54165665, 0.32654071), (-0.5518417, 0.32654071, -0.76736033)62.63442, 70.2124, 50.02191
12generate(0.30901699, -0.83998639, 0.44601722), (-0.83998638, -0.46098703, -0.2862059), (0.44601722, -0.2862059, -0.84802996)62.63442, 76.14089, -40.4294
13generate(-0.5, -0.36126761, 0.78707414), (-0.3612676, -0.73897143, -0.56868879), (0.78707414, -0.56868879, 0.23897142)135.96809, 32.74724, -71.34464
14generate(-1), (-0.99144486, -0.13052619), (-0.13052619, 0.99144486)181.29078
15generate(-0.5, -0.25544312, -0.8274955), (-0.25544312, -0.86949762, 0.42275607), (-0.8274955, 0.42275607, 0.36949762)135.96809, 23.15474, 75.00865
16generate(-0.99785893, -0.06540313), (-0.06540313, 0.0652631, -0.99572242), (0.99785892, 0.00427757, -0.0652631)90.64539, 5.92849, -90.45131
17generate(-0.30901699, -0.83998639, 0.44601722), (0.77458326, -0.49440059, -0.39444749), (0.5518417, 0.22358649, 0.80341758)118.65636, -70.2124, -50.02191
18generate(-0.80901699, -0.51914014, 0.27565379), (0.51914014, -0.41115427, 0.74929678), (-0.2756538, 0.74929679, 0.60213728)163.97905, -47.05766, 24.98675
19generate(-0.80901699, -0.47871879, -0.34105692), (-0.47871878, 0.19995846, 0.85489469), (-0.34105693, 0.8548947, -0.39094146)163.97905, 43.39365, 30.91524
20generate(-0.30901699, -0.77458326, -0.5518417), (-0.83998638, 0.49440059, -0.22358649), (0.44601722, 0.39444749, -0.80341758)118.65636, 76.14089, -40.4294
21generate(0.80901699, 0.51914014, -0.27565379), (0.47871878, -0.30983393, 0.82148113), (0.34105693, -0.79655285, -0.49918306)17.31173, -43.39365, -30.91524
22generate(0.80901699, 0.47871879, 0.34105692), (-0.51914014, 0.30983393, 0.79655284), (0.2756538, -0.82148114, 0.49918305)17.31173, 47.05766, -24.98675
23generate(0.30901699, 0.77458326, 0.5518417), (-0.77458326, 0.54165665, -0.32654071), (-0.5518417, -0.32654071, 0.76736033)62.63442, 70.2124, 50.02191
24generate(0.99785893, 0.06540313), (0.06540313, 0.0652631, -0.99572242), (-0.99785892, 0.00427757, -0.0652631)90.64539, -5.92849, 90.45131
25generate(0.30901699, 0.83998639, -0.44601722), (0.83998638, -0.46098703, -0.2862059), (-0.44601722, -0.2862059, -0.84802996)62.63442, -76.14089, 40.4294
26generate(-0.5, 0.36126761, -0.78707414), (-0.3612676, 0.73897143, 0.56868879), (0.78707414, 0.56868879, -0.23897142)135.96809, 32.74724, -71.34464
27generate(0.5, -0.25544312, -0.8274955), (-0.3612676, 0.80687821, -0.46736845), (0.78707414, 0.53263155, 0.31115577)45.3227, 32.74724, -71.34464
28generate(0.80901699, -0.51914014, 0.27565379), (0.47871878, 0.30983393, -0.82148113), (0.34105693, 0.79655285, 0.49918306)17.31173, -43.39365, -30.91524
29generate(-0.06540313, 0.99785892), (0.99785892, -0.0652631, -0.00427757), (0.06540313, 0.99572244, 0.0652631)90.64539, -90.45131, -5.92849
30generate(-0.80901699, 0.47871879, 0.34105692), (0.47871878, 0.19995846, 0.85489469), (0.34105693, 0.8548947, -0.39094146)163.97905, -43.39365, -30.91524

-
Components

-
HUMAN RHINOVIRUS 16 COAT ... , 4 types, 4 molecules 1234

#1: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 32501.375 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#2: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 28990.615 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#3: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 26314.168 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: Q82122
#4: Protein HUMAN RHINOVIRUS 16 COAT PROTEIN / HRV16


Mass: 7374.025 Da / Num. of mol.: 1 / Mutation: N-TERMINAL MYRISTOYLATION ON VP4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus sp. / Genus: Rhinovirus / Strain: SEROTYPE 16 / Cell line: HELA / Production host: Homo sapiens (human) / References: UniProt: P23008

-
Non-polymers , 4 types, 536 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlvirus1drop
20.25-0.75 %PEG80001drop
30.5-1.5 %PEG80001reservoir
45-20 mM1reservoirCaCl2
51reservoirNaCl

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 1452910 / % possible obs: 44.5 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.14→2.25 Å / Rmerge(I) obs: 0.24 / % possible all: 47
Reflection
*PLUS
Num. measured all: 3442752
Reflection shell
*PLUS
% possible obs: 47 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR
Starting model: PDB ENTRY 2RHN

2rhn
PDB Unreleased entry


Resolution: 2.15→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: DISORDERED SIDE CHAINS (1 1, 1 4, 1 5, 2 159, 2 160) WERE MODELLED WITH PREFERRED ROTAMERS WITH GOOD STEREOCHEMISTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 12388 10 %RANDOM
Rwork0.23 ---
obs0.23 1115369 44.5 %-
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 30 541 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22.5
Refine LS restraints NCSNCS model details: 30-FOLD, STRICT
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 9613 10 %
Rwork0.293 86834 -
obs--47 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR.AHTOP.AH
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.293

+
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