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- PDB-3dpr: Human rhinovirus 2 bound to a concatamer of the VLDL receptor mod... -

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Basic information

Entry
Database: PDB / ID: 3dpr
TitleHuman rhinovirus 2 bound to a concatamer of the VLDL receptor module V3
Components
  • LDL-receptor class A 3
  • Protein VP1
  • Protein VP2
  • Protein VP3
  • Protein VP4
KeywordsVIRUS / HUMAN RHINOVIRUS / VLDL-RECEPTOR / VIRUS-PROTEIN COMPLEX / ICOSAHEDRAL VIRUS / ATP-binding / Capsid protein / Covalent protein-RNA linkage / Cytoplasmic vesicle / Helicase / Host-virus interaction / Hydrolase / Lipoprotein / Membrane / Myristate / Nucleotide-binding / Nucleotidyltransferase / Phosphoprotein / Protease / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase / Virion / Cholesterol metabolism / Coated pit / EGF-like domain / Endocytosis / Glycoprotein / Lipid metabolism / Lipid transport / Receptor / Steroid metabolism / Transmembrane / Transport / VLDL
Function / homology
Function and homology information


reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway ...reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / very-low-density lipoprotein particle / cargo receptor activity / positive regulation of dendrite development / dendrite morphogenesis / lipid transport / regulation of synapse assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / apolipoprotein binding / clathrin-coated pit / receptor-mediated endocytosis / cholesterol metabolic process / VLDLR internalisation and degradation / ribonucleoside triphosphate phosphatase 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / memory / calcium-dependent protein binding / nervous system development / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / receptor complex / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / calcium ion binding / virion attachment to host cell / host cell nucleus / glutamatergic synapse / structural molecule activity / signal transduction / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / Jelly Rolls - #20 / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / Genome polyprotein / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Human rhinovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsQuerol-Audi, J. / Pous, J. / Fita, I. / Verdaguer, N.
CitationJournal: Febs Lett. / Year: 2009
Title: Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition
Authors: Querol-Audi, J. / Konecsni, T. / Pous, J. / Carugo, O. / Fita, I. / Verdaguer, N. / Blaas, D.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Refinement description
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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

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Assembly

Deposited unit
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9147
Polymers99,6745
Non-polymers2402
Water00
1
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,994,845420
Polymers5,980,421300
Non-polymers14,424120
Water0
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
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules
x 5


  • icosahedral pentamer
  • 500 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)499,57035
Polymers498,36825
Non-polymers1,20210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 599 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)599,48542
Polymers598,04230
Non-polymers1,44212
Water0
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
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules
x 30
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
E: LDL-receptor class A 3
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 5.99 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)5,994,845420
Polymers5,980,421300
Non-polymers14,424120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation58
transform to crystal frame1
Unit cell
Length a, b, c (Å)498.117, 498.117, 658.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.38548104, -0.9157036, 0.11353981), (0.76277549, 0.38548105, 0.51920893), (-0.51920893, -0.11353981, 0.84707189)192.87831, -18.68714, 79.7554
3generate(-0.60883151, -0.71886405, -0.33549766), (0.31849307, -0.6088315, 0.72655788), (-0.72655788, 0.33549765, 0.59962902)293.39653, 162.64188, 49.29155
4generate(-0.60883151, 0.31849307, -0.72655789), (-0.71886405, -0.60883151, 0.33549765), (-0.33549765, 0.72655788, 0.59962903)162.6419, 293.39652, -49.29154
5generate(0.38548105, 0.76277549, -0.51920893), (-0.91570359, 0.38548104, -0.11353981), (0.11353982, 0.51920893, 0.8470719)-18.68713, 192.87831, -79.7554
6generate(-0.42721408, 0.18404029, -0.88522162), (0.18404029, -0.94086651, -0.28442816), (-0.88522161, -0.28442816, 0.36808059)156.69699, 221.44077, 147.42958
7generate(0.43531346, 0.56265341, -0.7027968), (-0.49904823, -0.49891865, -0.7085415), (-0.7493017, 0.65916714, 0.06360519)0.25627, 251.83557, 11.3611
8generate(0.96188169, -0.10193046, -0.25375933), (-0.20505548, 0.34510424, -0.91589045), (0.18093056, 0.93301299, 0.31104806)17.65258, 108.39335, -140.40803
9generate(0.42479121, -0.891279, -0.15866373), (0.65973056, 0.42479121, -0.61992582), (0.61992581, 0.15866373, 0.76845157)184.8448, -10.65362, -98.13803
10generate(-0.43371719, -0.71453935, -0.54892889), (0.90020497, -0.36998242, -0.22966066), (-0.03899247, -0.59375628, 0.80369961)270.77897, 59.21353, 79.7554
11generate(-0.89127899, 0.42479122, 0.15866373), (0.42479121, 0.65973056, 0.61992582), (0.15866373, 0.61992581, -0.76845156)184.8448, -10.65363, -98.13802
12generate(-0.10193046, 0.9618817, 0.25375933), (0.34510424, -0.20505548, 0.91589045), (0.93301298, 0.18093055, -0.31104806)17.65258, 108.39334, -140.40803
13generate(0.56265341, 0.43531346, 0.7027968), (-0.49891865, -0.49904822, 0.7085415), (0.65916714, -0.74930171, -0.06360519)0.25627, 251.83556, 11.3611
14generate(0.18404029, -0.42721408, 0.88522162), (-0.94086651, 0.1840403, 0.28442816), (-0.28442816, -0.88522161, -0.36808059)156.69698, 221.44077, 147.42958
15generate(-0.71453935, -0.43371719, 0.54892889), (-0.36998241, 0.90020497, 0.22966066), (-0.59375628, -0.03899246, -0.80369961)270.77897, 59.21353, 79.75541
16generate(-0.36998242, -0.71453935, 0.59375629), (0.90020497, -0.43371719, 0.03899246), (0.22966065, 0.54892888, 0.80369961)262.74546, 67.24703, -98.13803
17generate(-0.99593788, -0.00406212, 0.08995132), (-0.00406212, -0.99593788, -0.08995132), (0.08995131, -0.08995131, 0.99187576)252.09184, 252.09183
18generate(-0.43371719, 0.90020497, -0.03899246), (-0.71453934, -0.36998243, -0.59375629), (-0.54892888, -0.22966065, 0.80369961)67.24704, 262.74546, 98.13803
19generate(0.53970977, 0.74859554, 0.38512088), (-0.24937133, 0.57910001, -0.77618111), (-0.80406921, 0.32287442, 0.49922421)-36.33971, 84.48497, 60.65264
20generate(0.57910002, -0.24937133, 0.77618111), (0.74859554, 0.53970976, -0.38512088), (-0.32287441, 0.80406921, 0.49922421)84.48496, -36.33971, -60.65264
21generate(-0.49904823, 0.43531347, 0.74930172), (-0.49891864, 0.56265341, -0.65916715), (-0.70854149, -0.70279679, -0.06360518)134.07942, 118.01241, 177.89343
22generate(-0.24937133, 0.53970977, 0.80406922), (0.57910002, 0.74859553, -0.32287442), (-0.7761811, 0.38512087, -0.4992242)89.44994, -41.30469, 49.29155
23generate(-0.10193046, 0.34510425, 0.933013), (0.96188169, -0.20505548, 0.18093055), (0.25375932, 0.91589045, -0.31104805)95.39485, 30.65106, -147.42957
24generate(-0.26048388, 0.12043511, 0.95793713), (0.12043511, -0.98038634, 0.15600642), (0.95793712, 0.15600642, 0.24087022)143.69849, 234.43926, -140.40803
25generate(-0.50591616, 0.17618748, 0.84439732), (-0.78238914, -0.50591616, -0.36320252), (0.3632025, -0.8443973, 0.39379833)167.60687, 288.43154, 60.65264
26generate(0.12043511, -0.26048388, -0.95793713), (-0.98038634, 0.12043511, -0.15600642), (0.15600643, 0.95793712, -0.24087022)143.6985, 234.43926, -140.40803
27generate(0.34510424, -0.10193046, -0.933013), (-0.20505547, 0.96188169, -0.18093055), (0.91589044, 0.25375932, 0.31104805)95.39486, 30.65106, -147.42958
28generate(0.53970977, -0.24937134, -0.80406922), (0.74859553, 0.57910002, 0.32287442), (0.38512087, -0.7761811, 0.4992242)89.44995, -41.30469, 49.29155
29generate(0.43531346, -0.49904823, -0.74930172), (0.56265341, -0.49891864, 0.65916715), (-0.70279679, -0.70854149, 0.06360518)134.07943, 118.0124, 177.89343
30generate(0.17618747, -0.50591616, -0.84439732), (-0.50591616, -0.78238915, 0.36320251), (-0.8443973, 0.36320251, -0.39379833)167.60688, 288.43154, 60.65265
31generate(-0.72079003, -0.42983001, 0.54378998), (-0.36327001, 0.90240002, 0.23176), (-0.59033, -0.03049, -0.80659002)270.31317, 57.42341, 407.7088
32generate(-0.8880553, 0.43259689, 0.15561926), (0.42796305, 0.65419178, 0.62360592), (0.16797069, 0.62039407, -0.76609638)182.69089, -11.02266, 230.08681
33generate(-0.09315309, 0.96228436, 0.25559924), (0.34019133, -0.21051287, 0.91649211), (0.93573498, 0.17232123, -0.30775321)15.73177, 109.0331, 189.79101
34generate(0.56538876, 0.42722232, 0.70556098), (-0.50528764, -0.49672149, 0.7056598), (0.65193872, -0.75548708, -0.06497519)0.16763, 251.6777, 342.50881
35generate(0.1774878, -0.43315168, 0.88367265), (-0.94005066, 0.1910965, 0.28247209), (-0.29122131, -0.88083132, -0.3732733)157.5076, 219.78116, 477.18942
36generate(-0.25254903, 0.11708907, 0.96047321), (0.11611307, -0.98181335, 0.15021284), (0.96059681, 0.14945943, 0.23435496)142.35638, 234.49653, 189.53891
37generate(-0.50672646, 0.16734373, 0.84570919), (-0.78213562, -0.50185073, -0.36934172), (0.36261666, -0.8486168, 0.38518215)168.06002, 287.21979, 390.7153
38generate(-0.50678751, 0.43249741, 0.74572921), (-0.49253237, 0.56468544, -0.66222791), (-0.70751226, -0.70290858, -0.07316102)134.64617, 116.28395, 507.23476
39generate(-0.25264782, 0.54611675, 0.79870222), (0.58470097, 0.74387844, -0.32368696), (-0.77090815, 0.38522027, -0.50725987)88.29165, -42.08346, 378.07136
40generate(-0.0955198, 0.35118367, 0.93142131), (0.96086453, -0.21191038, 0.17842904), (0.26003995, 0.91201267, -0.31720454)93.05682, 30.97593, 181.72452
41generate(0.54611675, -0.25264782, -0.79870222), (0.74387843, 0.58470096, 0.32368696), (0.38522027, -0.77090815, 0.50725986)88.29166, -42.08347, 378.07135
42generate(0.43249741, -0.50678752, -0.74572921), (0.56468544, -0.49253237, 0.66222791), (-0.70290858, -0.70751226, 0.07316101)134.64618, 116.28394, 507.23476
43generate(0.16734372, -0.50672646, -0.84570919), (-0.50185073, -0.78213562, 0.36934172), (-0.84861679, 0.36261666, -0.38518216)168.06002, 287.21978, 390.71531
44generate(0.11708907, -0.25254904, -0.96047321), (-0.98181334, 0.11611307, -0.15021285), (0.14945943, 0.96059681, -0.23435496)142.35639, 234.49653, 189.53891
45generate(0.35118367, -0.0955198, -0.93142131), (-0.21191038, 0.96086454, -0.17842904), (0.91201267, 0.26003995, 0.31720454)93.05683, 30.97593, 181.72452
46generate(0.42722232, 0.56538876, -0.70556098), (-0.49672149, -0.50528764, -0.7056598), (-0.75548708, 0.65193873, 0.06497519)0.16764, 251.67771, 342.50882
47generate(0.96228435, -0.0931531, -0.25559924), (-0.21051287, 0.34019133, -0.91649211), (0.17232123, 0.93573499, 0.30775321)15.73177, 109.03311, 189.791
48generate(0.43259688, -0.88805531, -0.15561926), (0.65419177, 0.42796305, -0.62360592), (0.62039407, 0.16797069, 0.76609638)182.69089, -11.02265, 230.0868
49generate(-0.42983001, -0.72079003, -0.54378998), (0.90240001, -0.36327002, -0.23176), (-0.03049, -0.59033, 0.80659002)270.31317, 57.42341, 407.70879
50generate(-0.43315167, 0.1774878, -0.88367265), (0.1910965, -0.94005066, -0.28247209), (-0.88083131, -0.29122131, 0.3732733)157.50761, 219.78116, 477.18942
51generate(0.0046317, 0.99995953, -0.00768994), (0.99997465, -0.00459592, 0.00575836), (0.00572248, -0.00772251, -0.99995712)-1.34241, -0.08488, 329.70907
52generate(0.76852274, 0.3820973, 0.51319986), (0.37897582, -0.91810583, 0.11602844), (0.51550203, 0.10531797, -0.85039543)-19.74875, 193.33368, 251.20514
53generate(0.32124745, -0.61471638, 0.72036344), (-0.61446363, -0.71411577, -0.33537547), (0.72058313, -0.33489525, -0.60713404)162.27277, 292.84056, 280.84259
54generate(-0.71907492, -0.6129189, 0.32750777), (-0.60744415, 0.32546693, -0.72462851), (0.33755066, -0.72000245, -0.60635191)293.17459, 160.92063, 377.66346
55generate(-0.91475422, 0.3850057, -0.12245397), (0.39033358, 0.76397431, -0.5137962), (-0.10425751, -0.51779857, -0.84912992)192.05485, -20.11725, 407.8646
56generate(0.89668881, -0.4412304, 0.03556057), (-0.37278785, -0.70936698, 0.59819002), (-0.23871986, -0.5496449, -0.8005685)67.87354, 261.77974, 428.82713
57generate(-0.00936656, -0.99522467, -0.09715852), (-0.99537599, -2.74E-6, 0.09607402), (-0.09561532, 0.09761534, -0.99062383)251.90683, 250.84197, 329.20488
58generate(-0.71229804, -0.3640319, -0.60009327), (-0.43358315, 0.9005601, -0.03163462), (0.55194143, 0.2376594, -0.79930299)260.94921, 66.51801, 229.93101
59generate(-0.24067822, 0.58006096, -0.77820494), (0.53621206, 0.7477743, 0.3915531), (0.80904898, -0.32304885, -0.49100489)82.50441, -36.46269, 268.19864
60generate(0.75373034, 0.53234966, -0.38534926), (0.57378562, -0.24721535, 0.78080613), (0.32039342, -0.80962967, -0.49178702)-36.82292, 84.21569, 391.1232

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Protein VP1 / Virion protein 1 / P1D / COAT PROTEIN VP1


Mass: 32924.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HeLa cells / Source: (natural) Human rhinovirus 2 / Strain: Human / References: UniProt: P04936
#2: Protein Protein VP2 / Virion protein 2 / P1B / COAT PROTEIN VP2


Mass: 29009.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HeLa cells / Source: (natural) Human rhinovirus 2 / Strain: Human / References: UniProt: P04936
#3: Protein Protein VP3 / Virion protein 3 / P1C / COAT PROTEIN VP3


Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HeLa cells / Source: (natural) Human rhinovirus 2 / Strain: Human / References: UniProt: P04936
#4: Protein Protein VP4 / Virion protein 4 / P1A / COAT PROTEIN VP4


Mass: 7356.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HeLa cells / Source: (natural) Human rhinovirus 2 / Strain: Human / References: UniProt: P04936

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Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide LDL-receptor class A 3 / VLDL-RECEPTOR MODULE 3 / V33333


Mass: 4274.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / References: UniProt: P98155

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.85 % / Mosaicity: 0.15 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 777511 / % possible obs: 48.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.199 / Χ2: 2.317 / Net I/σ(I): 5
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.462 / Num. unique all: 18810 / Χ2: 0.953 / % possible all: 11.8

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Phasing

PhasingMethod: molecular replacement
Phasing dmMethod: Solvent flattening / Reflection: 30955

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→15 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.441 31034 -RANDOM
Rwork0.425 ---
obs0.426 588726 61.6 %-
all-1005563 --
Displacement parametersBiso max: 30 Å2 / Biso mean: 22.543 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6435 0 15 0 6450
LS refinement shellResolution: 3.5→3.59 Å /
RfactorNum. reflection
Rfree0.465 -
Rwork0.46 -
obs-34661

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