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- PDB-2v9p: Crystal structure of papillomavirus E1 hexameric helicase DNA-fre... -

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Basic information

Entry
Database: PDB / ID: 2v9p
TitleCrystal structure of papillomavirus E1 hexameric helicase DNA-free form
ComponentsREPLICATION PROTEIN E1DNA replication
KeywordsHYDROLASE / AAA+ MOLECULAR MOTOR / DNA REPLICATION / DNA TRANSLOCATION / NUCLEOTIDE-BINDING / DNA-BINDING / REPLICATION / EARLY PROTEIN / ATPASE / NUCLEUS / HELICASE / ATP-BINDING
Function / homology
Function and homology information


DNA helicase activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Zinc finger, large T-antigen D1 domain / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Zinc finger, large T-antigen D1 domain superfamily ...Zinc finger, large T-antigen D1 domain / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Replication protein E1
Similarity search - Component
Biological speciesBOVINE PAPILLOMAVIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSanders, C.M. / Kovalevskiy, O.V. / Sizov, D. / Lebedev, A.A. / Isupov, M.N. / Antson, A.A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Papillomavirus E1 Helicase Assembly Maintains an Asymmetric State in the Absence of DNA and Nucleotide Cofactors.
Authors: Sanders, C.M. / Kovalevskiy, O.V. / Sizov, D. / Lebedev, A.A. / Isupov, M.N. / Antson, A.A.
History
DepositionAug 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
C: REPLICATION PROTEIN E1
D: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1
G: REPLICATION PROTEIN E1
H: REPLICATION PROTEIN E1
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
K: REPLICATION PROTEIN E1
L: REPLICATION PROTEIN E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,59636
Polymers415,74012
Non-polymers1,85524
Water63135
1
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
C: REPLICATION PROTEIN E1
D: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,79818
Polymers207,8706
Non-polymers92812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25740 Å2
ΔGint-86.7 kcal/mol
Surface area80390 Å2
MethodPQS
2
G: REPLICATION PROTEIN E1
H: REPLICATION PROTEIN E1
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
K: REPLICATION PROTEIN E1
L: REPLICATION PROTEIN E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,79818
Polymers207,8706
Non-polymers92812
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23560 Å2
ΔGint-111.8 kcal/mol
Surface area79750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)135.111, 180.649, 187.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31D
41H
51I
61J
12E
22K
13F
23L
14A
24G
15A
25B
35C
45G
55H
65I
16D
26E
36F
46J
56K
66L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B308 - 375
2112C308 - 375
3112D308 - 375
4112H308 - 375
5112I308 - 375
6112J308 - 375
1212B378 - 492
2212C378 - 492
3212D378 - 492
4212H378 - 492
5212I378 - 492
6212J378 - 492
1312B517 - 545
2312C517 - 545
3312D517 - 545
4312H517 - 545
5312I517 - 545
6312J517 - 545
1412B559 - 572
2412C559 - 572
3412D559 - 572
4412H559 - 572
5412I559 - 572
6412J559 - 572
1122E308 - 375
2122K308 - 375
1222E378 - 492
2222K378 - 492
1322E517 - 545
2322K517 - 545
1422E559 - 572
2422K559 - 572
1132F308 - 375
2132L308 - 375
1232F378 - 492
2232L378 - 492
1332F517 - 545
2332L517 - 545
1432F559 - 572
2432L559 - 572
1142A308 - 375
2142G308 - 375
1242A378 - 492
2242G378 - 492
1342A517 - 545
2342G517 - 545
1442A559 - 572
2442G559 - 572
1151A1580 - 1582
2151B1579 - 1581
3151C1579 - 1581
4151G1579 - 1581
5151H1579 - 1581
6151I1580 - 1582
1161D1580
2161E1579
3161F1580
4161J1578
5161K1580
6161L1579

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
REPLICATION PROTEIN E1 / DNA replication / ATP-DEPENDENT HELICASE E1 / E1 HELICASE


Mass: 34645.016 Da / Num. of mol.: 12 / Fragment: HELICASE DOMAIN, RESIDUES 301-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE PAPILLOMAVIRUS TYPE 1 / Strain: BPV-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03116, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.5 / Details: K-PHOSPHATE PH 7.5, NACL, PEG3350, MES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00806
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2004
RadiationMonochromator: SI 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00806 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 86088 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GXA
Resolution: 3→24.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 48.189 / SU ML: 0.385 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 853 1 %RANDOM
Rwork0.219 ---
obs0.219 85189 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.51 Å2
Baniso -1Baniso -2Baniso -3
1-6.93 Å20 Å20 Å2
2---4.97 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 3→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25948 0 96 35 26079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02226704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.93236202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59853200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94823.2261240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.969154354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.98615156
X-RAY DIFFRACTIONr_chiral_restr0.0850.23926
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0220188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.212390
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.218320
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2816
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5121.516339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01325797
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.559411835
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.731810405
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B896tight positional0.110.1
12C896tight positional0.070
13D896tight positional0.110
14H896tight positional0.080
15I896tight positional0.140
16J896tight positional0.140
21E896tight positional0.080.1
22K896tight positional0.080.1
31F896tight positional0.10.1
32L896tight positional0.10.1
41A896tight positional0.080.1
42G896tight positional0.080.1
51A11tight positional0.410.1
52B11tight positional0.260.01
53C11tight positional1.110
54G11tight positional0.250
55H11tight positional0.260
56I11tight positional0.260
61D5tight positional0.020.1
62E5tight positional0.020.02
63F5tight positional0.010
64J5tight positional0.020
65K5tight positional0.010
66L5tight positional0.020
11B913medium positional0.240.3
12C913medium positional0.230
13D913medium positional0.240
14H913medium positional0.270
15I913medium positional0.240
16J913medium positional0.270
21E917medium positional0.20.3
22K917medium positional0.20.3
31F913medium positional0.240.3
32L913medium positional0.240.3
41A913medium positional0.190.3
42G913medium positional0.190.3
11B896tight thermal0.775
12C896tight thermal0.750.01
13D896tight thermal0.620
14H896tight thermal0.850
15I896tight thermal0.860
16J896tight thermal0.70
21E896tight thermal0.615
22K896tight thermal0.615
31F896tight thermal1.215
32L896tight thermal1.215
41A896tight thermal0.735
42G896tight thermal0.735
51A11tight thermal3.385
52B11tight thermal3.650.45
53C11tight thermal3.70.04
54G11tight thermal1.410
55H11tight thermal1.230
56I11tight thermal1.920
61D5tight thermal0.735
62E5tight thermal0.91
63F5tight thermal3.540.2
64J5tight thermal4.890.04
65K5tight thermal1.240.01
66L5tight thermal7.660
11B913medium thermal1.2410
12C913medium thermal1.210.01
13D913medium thermal1.180
14H913medium thermal1.330
15I913medium thermal1.490
16J913medium thermal1.350
21E917medium thermal1.0610
22K917medium thermal1.0610
31F913medium thermal1.5310
32L913medium thermal1.5310
41A913medium thermal1.1110
42G913medium thermal1.1110
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 35
Rwork0.329 4228
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.96811.52230.62272.05820.75631.1916-0.18580.03870.0364-0.34590.0976-0.04630.12610.02860.08820.02540.00060.0154-0.29630.0213-0.160714.034449.081246.9625
22.93010.7213-0.30682.2638-0.2822.53790.0594-0.1565-0.12330.2218-0.0072-0.10.6607-0.266-0.0522-0.109-0.0943-0.039-0.21470.0724-0.251914.647650.931874.5373
31.0470.0491-0.66411.7563-0.52472.4549-0.0209-0.16880.07920.76320.026-0.1118-0.2157-0.0195-0.0051-0.01070.0131-0.0484-0.1719-0.0029-0.282714.834975.23287.3272
42.5164-0.7014-0.68742.36350.05171.9955-0.1299-0.05390.38240.64590.2466-0.0803-0.5726-0.0748-0.11670.13560.0589-0.0493-0.2103-0.0095-0.215313.688199.241973.0025
52.7881-1.3910.11792.4695-0.19611.11150.11190.14090.1849-0.0799-0.0963-0.1355-0.2809-0.0681-0.0155-0.1692-0.03340.032-0.27990.023-0.171213.277999.072544.2374
63.9041-1.26321.09561.5903-1.00241.85740.01420.1556-0.2498-0.0087-0.00450.08440.0640.0185-0.0097-0.191-0.02390.0443-0.3012-0.0406-0.167912.55873.265830.7087
74.4852.30611.18941.89410.77271.3546-0.15710.19850.1455-0.23810.15040.02210.21140.13410.0067-0.16970.01110.1094-0.21210.0104-0.148283.665164.037847.1363
82.41220.4572-0.49042.42870.11312.109-0.2633-0.1314-0.13490.30230.1437-0.02030.7847-0.1680.1196-0.12560.01020.0559-0.1980.0491-0.297583.825666.09974.5604
91.49160.0614-0.79011.6712-0.36022.0495-0.17-0.1440.13130.44260.1006-0.17560.12650.01380.0693-0.36310.0881-0.0839-0.1011-0.0192-0.290581.967190.43887.4469
102.7402-0.669-0.76042.0822-0.08042.2189-0.0748-0.02370.36510.22360.159-0.1759-0.4806-0.1338-0.0842-0.26570.0793-0.0986-0.185-0.0327-0.176379.1736114.118772.7144
111.9411-1.0776-0.11192.5497-0.12710.87050.1420.08590.1047-0.384-0.0978-0.0464-0.1013-0.0241-0.0442-0.09170.0585-0.0433-0.22130.0197-0.171878.8727113.766444.309
123.431-0.91981.13351.8-0.89671.69190.07950.1505-0.2098-0.5421-0.0640.27160.1386-0.0706-0.01550.29870.0565-0.0769-0.199-0.0359-0.169779.717987.874830.9285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A301 - 579
2X-RAY DIFFRACTION2B301 - 578
3X-RAY DIFFRACTION3C301 - 578
4X-RAY DIFFRACTION4D301 - 579
5X-RAY DIFFRACTION5E301 - 578
6X-RAY DIFFRACTION6F301 - 579
7X-RAY DIFFRACTION7G301 - 578
8X-RAY DIFFRACTION8H301 - 578
9X-RAY DIFFRACTION9I301 - 579
10X-RAY DIFFRACTION10J301 - 577
11X-RAY DIFFRACTION11K301 - 579
12X-RAY DIFFRACTION12L301 - 578

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