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- PDB-4dgj: Structure of a human enteropeptidase light chain variant -

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Basic information

Entry
Database: PDB / ID: 4dgj
TitleStructure of a human enteropeptidase light chain variant
ComponentsEnteropeptidase catalytic light chain
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


enteropeptidase / brush border / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / MAM domain signature. / SEA domain superfamily ...Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / MAM domain signature. / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SEA domain profile. / SEA domain / SEA domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Concanavalin A-like lectin/glucanase domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZahn, M. / Simeonov, P. / Straeter, N.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of a supercharged variant of the human enteropeptidase light chain.
Authors: Simeonov, P. / Zahn, M. / Strater, N. / Zuchner, T.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs ..._reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enteropeptidase catalytic light chain
B: Enteropeptidase catalytic light chain
C: Enteropeptidase catalytic light chain
D: Enteropeptidase catalytic light chain


Theoretical massNumber of molelcules
Total (without water)105,5194
Polymers105,5194
Non-polymers00
Water16,628923
1
A: Enteropeptidase catalytic light chain


Theoretical massNumber of molelcules
Total (without water)26,3801
Polymers26,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enteropeptidase catalytic light chain


Theoretical massNumber of molelcules
Total (without water)26,3801
Polymers26,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Enteropeptidase catalytic light chain


Theoretical massNumber of molelcules
Total (without water)26,3801
Polymers26,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Enteropeptidase catalytic light chain


Theoretical massNumber of molelcules
Total (without water)26,3801
Polymers26,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.181, 147.704, 148.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Enteropeptidase catalytic light chain


Mass: 26379.672 Da / Num. of mol.: 4 / Mutation: N6D, G21D, G22D, C112S, N142D, K210E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS15, ENTK, PRSS7 / Production host: Escherichia coli (E. coli) / References: UniProt: P98073, enteropeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 16% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 91520 / % possible obs: 97.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 5 / Num. unique obs: 12289 / % possible all: 91.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.901 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21022 1829 2 %RANDOM
Rwork0.1689 ---
obs0.16972 89514 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.6 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 0 923 8309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.027698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.94310530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39824.324377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.147151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2251550
X-RAY DIFFRACTIONr_chiral_restr0.1650.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216050
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 107 -
Rwork0.223 5588 -
obs--86.96 %
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)
12.1969-0.531-0.40642.76370.4080.3380.04960.03510.0707-0.1269-0.0080.2635-0.002-0.0684-0.04160.05440.0142-0.0250.06750.0230.052127.352484.30373.0359
22.84520.8681.34964.5537-0.57288.1107-0.0578-0.06810.2543-0.18690.039-0.1591-0.08350.44260.01880.0698-0.02520.01930.0969-0.00580.047744.302592.743476.4072
30.14520.0442-0.0861.00710.05321.12350.02950.03320.05720.0544-0.0402-0.0039-0.14160.10230.01070.0514-0.00580.01020.05290.00850.031237.957491.598582.028
41.201-0.56720.64861.925-1.07661.51560.0320.00550.1377-0.06870.0107-0.0322-0.08290.0765-0.04270.0544-0.01540.01830.0131-0.0080.029536.298494.211483.7549
50.9446-1.16370.44445.769-1.32940.9196-0.0247-0.14440.07620.05440.1015-0.1865-0.04150.0703-0.07680.0367-0.0120.01530.07-0.03410.044839.482286.771890.4428
60.48850.2172-0.26831.0955-0.27320.65380.01610.06530.011-0.0438-0.01080.1530.0072-0.0686-0.00530.02190.0057-0.00940.042-0.00040.025128.030680.40779.5874
76.13720.9657-2.49065.50231.3882.80290.0206-0.0785-0.12110.0485-0.0914-0.07110.25430.0020.07080.07190.01790.00080.04640.01990.028338.885763.042887.6169
80.7968-0.0065-0.01890.4647-0.16260.51470.01630.0079-0.0119-0.0730.00410.01430.1123-0.0006-0.02040.05970.0021-0.01390.042-0.00420.009534.219472.471381.5784
914.8502-0.0432-3.82625.14682.59366.84530.0756-0.32770.16070.0568-0.20180.7695-0.0481-0.34550.12620.0048-0.00390.00310.1006-0.02550.160316.96979.372484.1622
100.319-0.1388-0.16691.13610.19120.97270.0335-0.05090.0033-0.02260.01740.04340.03030.0034-0.05090.01460.00290.00310.0471-0.00030.029632.851378.167787.8414
111.6331.194-0.06391.64270.68131.82910.0262-0.0496-0.00280.198-0.04310.15370.064-0.06610.01690.0734-0.00260.03780.04840.00780.05130.189763.0624130.8798
121.6936-0.5125-1.18997.14442.58614.8477-0.17130.06480.07540.46360.3721-0.54050.48540.7846-0.20080.0720.0446-0.02690.0739-0.02450.058546.924754.7397126.3076
130.7717-0.3274-0.42611.7748-0.02340.9761-0.04390.0139-0.0079-0.09390.0136-0.07120.13410.10480.03030.06860.00310.02250.0414-0.00560.02740.868356.5374116.8115
140.60570.04030.77051.16820.3351.05960.0915-0.0908-0.0540.1885-0.03980.00570.1829-0.1149-0.05170.0950.00330.01690.04850.01270.034538.563953.7727129.4777
151.10630.4509-0.77132.5518-0.69632.5675-0.0683-0.0263-0.0668-0.0247-0.0143-0.11880.19190.01470.08250.01680.00660.0030.015-0.00530.011239.364954.8287118.1929
162.6489-2.332-0.19714.59661.95091.26550.11910.21020.2253-0.2092-0.0202-0.2934-0.10410.1104-0.09890.0882-0.01190.04450.07790.01050.044343.681569.8178110.035
170.80160.104-0.18052.2670.5610.6766-0.00610.0251-0.0427-0.1272-0.02620.23060.0962-0.13630.03230.0471-0.0258-0.01820.04660.00080.041227.28558.2064117.6125
180.3785-0.49670.5551.248-1.02831.37310.0356-0.02950.04010.0912-0.03230.0937-0.02970.014-0.00330.0728-0.00260.02870.0568-0.01790.043535.40670.8015128.837
194.43622.01590.45413.01620.4342.63070.0222-0.066-0.00640.00230.0345-0.0357-0.1644-0.0067-0.05680.07-0.00620.02960.01160.00470.021440.407784.0606115.1663
200.35630.09640.20771.39370.16340.75090.0161-0.01320.0361-0.0083-0.02390.1128-0.0816-0.0430.00770.0277-0.00360.01720.0431-0.00670.025433.342670.8406118.0717
211.0187-0.1573-0.42030.57680.0650.5179-0.01050.05190.0542-0.0149-0.0519-0.02110.02950.05590.06240.0162-0.00040.01110.0320.01640.047265.0866100.3715103.8197
222.34020.3370.4560.53680.16790.8929-0.03040.2020.0639-0.1124-0.0141-0.04570.05170.06590.04450.03470.00960.02480.02320.00860.047564.66695.989598.7296
2312.61464.00630.518814.4709-0.856215.42460.2757-0.04020.9287-0.2797-0.22810.5858-0.7368-0.8548-0.04760.09320.0444-0.0110.0536-0.00080.093642.445499.1785100.6614
241.2557-0.53040.12260.50340.14150.4353-0.00180.0115-0.0749-0.0352-0.0005-0.0410.10130.0320.00230.06110.01030.03020.03140.01170.057567.033190.5037103.9192
253.3935-3.0808-1.07348.67642.39011.2207-0.1546-0.0189-0.4439-0.19910.00740.19910.05560.02780.14720.0937-0.03830.04750.08780.04870.118652.94484.9632119.1068
261.22270.3093-1.15161.1707-0.53431.62820.0965-0.17850.10070.0487-0.07760.0343-0.01790.0846-0.01890.0253-0.02570.01670.0517-0.0190.057260.0801105.3463115.6482
272.7665-1.3558-0.76144.14851.5321.27570.0308-0.08060.0277-0.0176-0.11790.16070.0234-0.04850.08710.0222-0.0230.02380.0354-0.02540.05141.668595.8841114.2583
282.7837-1.0932-2.8483.05970.09813.36380.0545-0.05880.02060.0868-0.06530.0359-0.07740.03690.01090.0167-0.03220.00730.0798-0.03740.05954.1284102.8009116.8156
291.7239-1.1329-1.351318.5906-3.029111.2836-0.0431-0.2744-0.01410.5178-0.3196-0.62980.78030.52520.36270.17450.0201-0.01680.13230.06080.053163.165185.7314120.6222
300.9777-0.2184-0.54851.43411.12071.2751-0.003-0.0579-0.0840.003-0.08560.0790.0273-0.05680.08860.0267-0.01250.01650.02380.00060.037752.841193.412110.2759
310.54870.88410.78862.6230.27392.6178-0.02830.15950.0013-0.237-0.194-0.1826-0.01530.43270.22230.08180.0950.06860.26210.04790.149465.958347.294184.1294
320.9476-0.06890.56750.9472-0.92571.3042-0.04730.01310.00450.0741-0.1191-0.1376-0.0360.16880.16640.03920.01520.02610.05810.06160.123464.29747.4506100.4305
338.49636.6008-3.910218.47162.31373.9469-0.0346-0.6637-0.3703-0.54230.0948-0.8278-0.18960.5454-0.06020.06860.05220.04340.28910.18260.265878.11345.008392.2937
341.8308-0.63250.51650.9853-0.82852.3074-0.0309-0.27140.00040.2189-0.0031-0.0226-0.136-0.19180.0340.093-0.00370.01930.0930.01940.083553.934352.5951103.4061
350.98870.21520.32620.8078-0.25550.43480.00450.13010.13770.0854-0.0957-0.2182-0.10340.12450.09130.0348-0.0277-0.00760.10430.09450.152269.552457.349795.4671
362.56391.2438-0.5982.0061-2.45483.7542-0.00880.04390.3545-0.0118-0.1340.0345-0.21540.09090.14280.19430.1049-0.01860.14080.060.124251.419461.802382.6613
371.5912-0.49250.81951.6883-0.26160.75690.04980.2463-0.1914-0.2462-0.08190.00080.12480.16160.03220.1030.06140.04820.0898-0.00790.076957.388342.529385.163
381.1455-0.63530.44682.49140.92992.73440.13360.0548-0.1705-0.1907-0.06490.23910.06-0.2057-0.06870.02830.0068-0.03020.0396-0.00850.063742.31248.77485.8149
391.7660.14830.83141.3840.32621.87340.08890.31670.0304-0.1656-0.19810.0587-0.07170.29320.10920.08030.05090.03460.1310.03240.061157.990852.698885.1172
401.4343-0.59640.90510.6707-0.01761.83410.02430.0566-0.041-0.015-0.0985-0.0372-0.0572-0.03550.07420.03790.01710.01490.02230.01840.050251.725153.776391.0066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 23
3X-RAY DIFFRACTION3A24 - 64
4X-RAY DIFFRACTION4A65 - 84
5X-RAY DIFFRACTION5A85 - 101
6X-RAY DIFFRACTION6A102 - 154
7X-RAY DIFFRACTION7A155 - 165
8X-RAY DIFFRACTION8A166 - 191
9X-RAY DIFFRACTION9A192 - 198
10X-RAY DIFFRACTION10A199 - 235
11X-RAY DIFFRACTION11B1 - 17
12X-RAY DIFFRACTION12B18 - 23
13X-RAY DIFFRACTION13B24 - 51
14X-RAY DIFFRACTION14B52 - 64
15X-RAY DIFFRACTION15B65 - 86
16X-RAY DIFFRACTION16B87 - 94
17X-RAY DIFFRACTION17B95 - 123
18X-RAY DIFFRACTION18B124 - 154
19X-RAY DIFFRACTION19B155 - 165
20X-RAY DIFFRACTION20B166 - 235
21X-RAY DIFFRACTION21C1 - 64
22X-RAY DIFFRACTION22C65 - 85
23X-RAY DIFFRACTION23C86 - 89
24X-RAY DIFFRACTION24C90 - 114
25X-RAY DIFFRACTION25C115 - 125
26X-RAY DIFFRACTION26C126 - 152
27X-RAY DIFFRACTION27C153 - 172
28X-RAY DIFFRACTION28C173 - 191
29X-RAY DIFFRACTION29C192 - 198
30X-RAY DIFFRACTION30C199 - 234
31X-RAY DIFFRACTION31D1 - 17
32X-RAY DIFFRACTION32D18 - 63
33X-RAY DIFFRACTION33D64 - 71
34X-RAY DIFFRACTION34D72 - 92
35X-RAY DIFFRACTION35D93 - 113
36X-RAY DIFFRACTION36D114 - 126
37X-RAY DIFFRACTION37D127 - 154
38X-RAY DIFFRACTION38D155 - 180
39X-RAY DIFFRACTION39D181 - 198
40X-RAY DIFFRACTION40D199 - 234

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  • 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

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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

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