[English] 日本語
Yorodumi
- PDB-1fpv: STRUCTURE DETERMINATION OF FELINE PANLEUKOPENIA VIRUS EMPTY PARTICLES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fpv
TitleSTRUCTURE DETERMINATION OF FELINE PANLEUKOPENIA VIRUS EMPTY PARTICLES
ComponentsFELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2
KeywordsVIRUS / PANLEUKEMIA VIRUS COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesFeline panleukopenia virus
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsAgbandje, M. / Rossmann, M.G.
Citation
Journal: Proteins / Year: 1993
Title: Structure determination of feline panleukopenia virus empty particles.
Authors: Agbandje, M. / McKenna, R. / Rossmann, M.G. / Strassheim, M.L. / Parrish, C.R.
#1: Journal: To be Published
Title: Determination and Refinement of the Canine Parvovirus Empty Capsid Structure
Authors: Wu, H. / Keller, W. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: The Canine Parvovirus Empty Capsid Structure
Authors: Wu, H. / Rossmann, M.G.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of Monoclinic Canine Parvovirus
Authors: Tsao, J. / Chapman, M.S. / Wu, H. / Agbandje, M. / Keller, W. / Rossmann, M.G.
#4: Journal: Virology / Year: 1991
Title: Mapping Specific Functions in the Capsid Structure of Canine Parvovirus and Feline Panleukopenia Virus Using Infectious Plasmid Clones
Authors: Parrish, C.R.
#5: Journal: Science / Year: 1991
Title: The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W. / Parrish, C.R.
#6: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Crystallographic Analysis of Canine Parvovirus Crystals
Authors: Luo, M. / Tsao, J. / Rossmann, M.G. / Basak, S. / Compans, R.W.
History
DepositionMar 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
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[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _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_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Remark 700SHEET THE STRUCTURE OF FELINE PANLEUKOPENIA VIRUS FOLLOWS THE CANONICAL PICORNAVIRUS "JELLY ROLL" ...SHEET THE STRUCTURE OF FELINE PANLEUKOPENIA VIRUS FOLLOWS THE CANONICAL PICORNAVIRUS "JELLY ROLL" BARREL. THE SHEET IDENTIFIED AS "BDG" IS THAT REFERRED TO AS "BIDG" IN THE LITERATURE WITH STRANDS 1 TO 5 CORRESPONDING TO STRANDS A, B, I, D, AND G. THE SHEET IDENTIFIED AS "CHF" IS THE SO-CALLED CHEF SHEET WITH STRANDS 1 TO 4 CORRESPONDING TO STRANDS C, H, E, AND F. THESE TWO SHEETS ARE LOOSELY CONNECTED TOGETHER BY HYDROGEN BONDS BETWEEN STRAND 4 OF "CHF" AND RESIDUE 45 IMMEDIATELY PRECEDING STRAND 1 OF "BDG" OF A FIVE-FOLD RELATED PROTOMER THAT IS NOT EXPLICITLY PRESENTED ON THE ATOM RECORDS, BUT WHICH CAN BE GENERATED USING THE SYMMETRY OPERATORS LISTED BELOW. FPV CONTAINS SEVERAL LONG LOOPS BETWEEN STRANDS OF "BDG" AND "CHF" WITH LITTLE ORGANIZED SECONDARY STRUCTURE. THERE ARE STRANDS WITHIN THE LOOPS THAT ARE LOOSELY HYDROGEN-BONDED TOGETHER. WITH FEWER HYDROGEN BONDS AND LESS REGULAR SECONDARY STRUCTURE THEY MUST BE REGARDED MORE TENTATIVELY UNTIL THE STRUCTURE IS REFINED. THIS IS WHY THE SHEET "LP2" HAS BEEN IDENTIFIED SEPARATELY, ALTHOUGH IT COULD BE CONSIDERED TO BE AN EXTENSION OF SHEET "CHF", EXTENDING FROM STRAND 1. STRAND 1 OF "LP2" HAS A BULGE AND A CHANGE OF DIRECTION AT RESIDUE 107, AFTER WHICH IT BECOMES STRAND 1 OF "CHF". THE MIDDLE STRAND OF "LP2" CONTAINS TWO SEGMENTS THAT RUN IN THE SAME GENERAL DIRECTION, BUT ARE SEPARATED BY NON-BETA STRUCTURE. THE FIRST SEGMENT (206 TO 211) HYDROGEN BONDS ON ONE SIDE ONLY, TO RESIDUES 103 TO 111, AND THE SECOND SEGMENT (215 TO 218) HYDROGEN BONDS ON THE OPPOSITE SIDE TO RESIDUES 230 TO 235. IN ORDER TO REPRESENT THE BIFURCATED SHEET STRUCTURE IN THE *SHEET* RECORDS BELOW, TWO SHEETS, *BDG* AND *CDG* ARE DEFINED. STRANDS 1 - 4 OF THESE SHEETS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)64,7641
Polymers64,7641
Non-polymers00
Water00
1
A: FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2
x 60


Theoretical massNumber of molelcules
Total (without water)3,885,82260
Polymers3,885,82260
Non-polymers00
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: FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2
x 5


  • icosahedral pentamer
  • 324 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)323,8185
Polymers323,8185
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2
x 6


  • icosahedral 23 hexamer
  • 389 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)388,5826
Polymers388,5826
Non-polymers00
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: FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2
x 60


  • crystal asymmetric unit, crystal frame
  • 3.89 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,885,82260
Polymers3,885,82260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)380.100, 379.300, 350.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 161 / 2: CIS PROLINE - PRO 423 / 3: CIS PROLINE - PRO 465
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.34816396, -0.81741617, -0.45919745), (0.92408404, 0.38184454, 0.02095686), (0.15771244, -0.43140753, 0.88802549)365.83309, -56.37449, 75.15858
3generate(-0.70656424, -0.39861951, -0.58478552), (0.67789436, -0.61859693, -0.39772455), (-0.20369437, -0.67674818, 0.70712718)504.77178, 261.73483, 223.91813
4generate(-0.70658608, 0.67762723, -0.20320577), (-0.39834328, -0.6187483, -0.67744075), (-0.58476848, -0.39696952, 0.70730039)224.80752, 514.71169, 240.698
5generate(0.34812862, 0.92398764, 0.15821157), (-0.81730503, 0.38159962, -0.43163345), (-0.45887845, 0.02128387, 0.88830574)-87.1586, 352.95067, 102.30899
6generate(-0.95018808, -0.06756695, -0.30414765), (-0.06756779, -0.90834825, 0.4125636), (-0.30438266, 0.41287721, 0.85853633)435.9305, 317.01857, 0.96847
7generate(-0.44122665, 0.88211061, 0.16481709), (-0.79784838, -0.46959985, 0.37835782), (0.41096002, 0.03608318, 0.91082649)69.27001, 374.5154, -69.13414
8generate(0.68751882, 0.62639158, 0.36745819), (-0.65206005, 0.30963362, 0.69252), (0.32007402, -0.71508461, 0.62088154)-129.48642, 137.54635, 147.63089
9generate(0.87616047, -0.48132904, 0.02373256), (0.16832269, 0.35247798, 0.92088867), (-0.45143929, -0.8025378, 0.38939554)114.33585, -66.40541, 351.70166
10generate(-0.13599806, -0.910219, -0.39134269), (0.52955877, -0.40027621, 0.74786609), (-0.83737475, -0.10541906, 0.53627427)463.78272, 44.51453, 261.05931
11generate(-0.92215431, 0.37999369, -0.07161279), (0.38025628, 0.85617177, -0.34981014), (-0.0717254, -0.35011828, -0.93401746)301.16973, 18.21042, 424.01099
12generate(0.01879098, 0.92977665, 0.36782039), (0.86839678, 0.16700761, -0.46731036), (-0.49581708, 0.32788092, -0.80383257)-62.98909, 82.76327, 347.30977
13generate(0.92374395, 0.1809896, 0.33749031), (0.38297288, -0.44446942, -0.81024915), (0.0035895, 0.87726786, -0.47927453)-80.88555, 355.91419, 87.02444
14generate(0.54209037, -0.83156922, -0.12068789), (-0.40517611, -0.13321885, -0.90469675), (0.73633141, 0.53880846, -0.40887151)272.21265, 460.1779, 2.86048
15generate(-0.59873749, -0.70857792, -0.37352752), (-0.40685506, 0.67062161, -0.62012979), (0.68978424, -0.21975789, -0.6899181)508.3358, 251.46549, 211.12962
16generate(0.87234238, -0.31242674, 0.37576044), (-0.31268848, -0.94782352, -0.06275346), (0.37610807, -0.06275894, -0.92451886)19.57025, 455.05929, 280.84513
17generate(0.07427171, -0.99447109, -0.07344003), (-0.99463244, -0.0792523, 0.06799568), (-0.07285538, 0.06744342, -0.99501941)384.55648, 389.38411, 352.49039
18generate(-0.90469854, -0.40876166, -0.12016298), (-0.40880719, 0.75343274, 0.5154537), (-0.11996915, 0.51456493, -0.8487342)462.27067, 35.09291, 247.25114
19generate(-0.71166475, 0.63527103, 0.3001611), (0.6351967, 0.39948917, 0.66124883), (0.29987637, 0.66069886, -0.68782442)145.31446, -118.1959, 110.56446
20generate(0.38660693, 0.69480928, 0.60665864), (0.69460133, -0.65194502, 0.30389715), (0.60646896, 0.30389308, -0.73466191)-128.28945, 141.3576, 131.32669
21generate(0.37475758, -0.08717932, -0.92329592), (0.86445826, -0.32701536, 0.38172769), (-0.33532388, -0.94064726, -0.04774222)298.42106, 31.29546, 434.15861
22generate(-0.09569918, 0.05869496, -0.99382504), (0.05898674, -0.99617138, -0.06482633), (-0.99351435, -0.0644855, 0.09187055)371.04086, 394.66833, 360.9263
23generate(-0.13581849, 0.529382, -0.83736709), (-0.91023293, -0.40063275, -0.10553061), (-0.39100679, 0.74785761, 0.53645123)258.02756, 467.53403, 8.00608
24generate(0.30984315, 0.67440833, -0.67014164), (-0.70377212, 0.63658639, 0.31586677), (0.63955385, 0.3737515, 0.67160444)115.56169, 149.19464, -136.87832
25generate(0.62539653, 0.29335247, -0.72324857), (0.39304735, 0.68208444, 0.61700896), (0.67396777, -0.6698019, 0.31055302)140.52625, -120.41562, 126.49843
26generate(-0.0691644, -0.3273399, -0.94263173), (-0.91549351, 0.39624168, -0.07011049), (0.39671012, 0.85738043, -0.32707728)433.25767, 304.83893, -10.26819
27generate(-0.47523487, 0.33820158, -0.8121809), (0.03636147, 0.92988811, 0.36643636), (0.87882758, 0.14421236, -0.45465324)355.5618, -57.68621, 61.94445
28generate(0.018976, 0.86798604, -0.49592307), (0.92974608, 0.16726683, 0.32819526), (0.36753597, -0.46716034, -0.80427681)101.59685, -69.26511, 341.14767
29generate(0.73048557, 0.52986938, -0.4309158), (0.53003316, -0.83770547, -0.13198588), (-0.4305771, -0.13184139, -0.89278011)22.33376, 286.10388, 441.49211
30generate(0.67601182, -0.20888268, -0.70699693), (-0.61038762, -0.69619123, -0.37815238), (-0.41254647, 0.68676983, -0.59785457)227.31141, 517.3129, 224.30516
31generate(-0.31251103, 0.39102783, 0.86603328), (-0.94889312, -0.08514248, -0.30405331), (-0.04504233, -0.91606116, 0.3976535)18.21151, 447.54577, 295.7964
32generate(0.38912171, 0.03115013, 0.92075861), (-0.45700218, 0.87430027, 0.16393789), (-0.79948471, -0.48452533, 0.354612)-53.06952, 82.35692, 360.84797
33generate(0.30947857, -0.70340207, 0.63962623), (0.67467028, 0.63668371, 0.37375784), (-0.67016717, 0.31551609, 0.67187171)156.73092, -121.79649, 122.33701
34generate(-0.44137633, -0.79750259, 0.41115154), (0.88219139, -0.46961416, 0.03544251), (0.16419786, 0.37843305, 0.91099049)357.67575, 117.21862, -90.12244
35generate(-0.82578704, -0.12110772, 0.55107878), (-0.12122597, -0.91572727, -0.38346782), (0.55054625, -0.38272355, 0.74151431)272.06605, 469.09149, 17.08135
36generate(0.00691784, 0.02349139, 0.99989437), (0.99992837, 0.01591615, -0.00756389), (-0.01634391, 0.99932799, -0.02283399)6.78024, 6.60811, -13.86221
37generate(0.18181233, -0.42804666, 0.88524733), (0.36165396, -0.808017, -0.46554793), (0.91417148, 0.40479846, 0.00817069)83.13734, 370.94924, -77.89413
38generate(-0.19263608, -0.69396598, 0.69366393), (-0.69418343, -0.40331779, -0.5964225), (0.69363798, -0.59621336, -0.40404613)240.31516, 513.81585, 234.33384
39generate(-0.5989524, -0.40677512, 0.68990591), (-0.70845243, 0.67073323, -0.2193234), (-0.37317461, -0.62034317, -0.68981482)261.09928, 237.77114, 491.33325
40generate(-0.4756213, 0.03663793, 0.87916672), (0.33856624, 0.92983406, 0.14461125), (-0.81196755, 0.36575562, -0.45421276)116.76676, -75.70048, 337.93966
41generate(0.37468354, 0.86433364, -0.3352107), (-0.08673125, -0.32749494, -0.94120612), (-0.92280635, 0.381748, -0.04718861)6.67143, 444.76427, 283.92521
42generate(0.87630133, 0.16838111, -0.45161566), (-0.48126945, 0.35188678, -0.80285152), (0.02403709, 0.92044274, 0.38984588)69.82274, 360.75775, -78.73537
43generate(0.38946944, -0.45717707, -0.79991282), (0.03099262, 0.87411966, -0.48458048), (0.92041883, 0.16363528, 0.35444489)346.96757, 104.51484, -92.53103
44generate(-0.41302701, -0.14784077, -0.89876734), (0.74212617, 0.51749561, -0.42623275), (0.52756978, -0.84279219, -0.1044686)455.10119, 30.15454, 261.60336
45generate(-0.4221652, 0.66889777, -0.61156563), (0.66936882, -0.22514305, -0.70844291), (-0.61160602, -0.70799112, -0.35269176)244.78661, 240.44025, 494.2661
46generate(-0.31238862, -0.94883304, -0.04515709), (0.39102594, -0.08526295, -0.91679302), (0.86540911, -0.30389202, 0.39765157)443.69259, 302.22197, 2.62128
47generate(-0.99268576, -0.08747409, 0.08346286), (-0.08723865, 0.0433233, -0.99548053), (0.0831971, -0.99498879, -0.05063755)379.50652, 381.17398, 366.23525
48generate(-0.41328768, 0.74202938, 0.52812273), (-0.14733863, 0.51731084, -0.84304441), (-0.8984732, -0.42609227, -0.10402316)27.55348, 271.99797, 448.95764
49generate(0.62509715, 0.39333177, 0.6743177), (0.2937821, 0.68166501, -0.67014619), (-0.72296679, 0.6166019, 0.31127182)-125.7794, 125.57146, 136.46892
50generate(0.6874562, -0.65167867, 0.32001129), (0.62650971, 0.30925392, -0.71572534), (0.36717242, 0.6921258, 0.62132386)131.40871, 144.25092, -139.38213
51generate(0.00719537, 0.99975884, -0.01609215), (0.02295598, 0.01618422, 0.99987507), (0.99951654, -0.00729714, -0.02337959)-6.87837, 13.59789, -7.05283
52generate(0.92382842, 0.38281311, 0.00335746), (0.18064076, -0.44393836, 0.87771238), (0.33756522, -0.80972122, -0.47989005)-61.81642, 96.23276, 357.25759
53generate(0.67592476, -0.61042563, -0.41321558), (-0.20891761, -0.69582584, 0.68717765), (-0.70640704, -0.37809071, -0.59813289)254.82203, 253.31155, 490.32988
54generate(-0.39392118, -0.6073352, -0.6901215), (-0.60736268, -0.39137828, 0.69158338), (-0.68966606, 0.6910957, -0.21470054)505.4534, 267.7567, 208.26266
55generate(-0.80721866, 0.38781353, -0.44468572), (-0.46405693, 0.04866814, 0.88484101), (0.36465269, 0.92025873, 0.14051654)343.71366, 119.60551, -99.13676
56generate(-0.06949029, -0.91525944, 0.39645994), (-0.32725067, 0.39657366, 0.85812408), (-0.9421193, -0.07055885, -0.32708337)313.18484, 29.70415, 426.33094
57generate(-0.80744399, -0.46372013, 0.36479534), (0.38786733, 0.04872829, 0.92061966), (-0.4447994, 0.88426727, 0.14068172)369.15764, -47.87622, 61.06712
58generate(-0.65210651, 0.32557332, 0.68500567), (0.32526362, -0.69560465, 0.64044723), (0.6844614, 0.64054769, 0.34771117)127.3274, 160.46392, -140.93189
59generate(0.18185103, 0.36184419, 0.91457114), (-0.42854559, -0.80778234, 0.40479556), (0.88506307, -0.4649054, 0.00789732)-78.10471, 366.80558, 99.48967
60generate(0.54192766, -0.40503263, 0.73624007), (-0.83182161, -0.13277902, 0.53932724), (-0.12021909, -0.90439341, -0.40914864)36.7615, 285.9916, 450.07738

-
Components

#1: Protein FELINE PANLEUKOPENIA VIRUS (STRAIN B) VIRAL PROTEIN 2


Mass: 64763.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline panleukopenia virus / Genus: Parvovirus / Strain: STRAIN B / References: UniProt: P24840
Compound detailsINTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, ...INTERPRETABLE ELECTRON DENSITY BEGINS AT THE 37TH RESIDUE OF VP2. THERE IS DIFFUSE DENSITY, SUGGESTING THAT ONE IN FIVE OF THE N-TERMINI IS ON THE OUTSIDE OF THE CAPSID, AND THAT THE POLYPEPTIDE RUNS DOWN THE FIVE-FOLD AXIS TO JOIN RESIDUE 37 ON THE INSIDE SURFACE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.75 %(w/v)PEG80001reservoir
28 mM1reservoirCaCl2
310 mMTris-HCl1reservoir
50.75 %(w/v)PEG80001drop
68 mM1dropCaCl2
710 mMTris-HCl1drop
4virus1drop0.005ml

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementHighest resolution: 3.3 Å
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 0 0 4350

+
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