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- PDB-5ikc: X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in... -

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Basic information

Entry
Database: PDB / ID: 5ikc
TitleX-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB
Components
  • Ighg protein
  • MAb 6H10 light chain
  • Neuronal migration protein doublecortinDevelopment of the nervous system
KeywordsTRANSFERASE / DCX DOMAIN / UBIQUITIN-LIKE FOLD / MICROTUBULE ASSOCIATED / SIGNALING PROTEIN
Function / homology
Function and homology information


axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton ...axoneme assembly / Neurofascin interactions / microtubule associated complex / central nervous system development / neuron migration / retina development in camera-type eye / nervous system development / microtubule binding / microtubule / cytoskeleton / neuron projection / intracellular signal transduction / protein kinase binding / cytosol
Similarity search - Function
Doublecortin domain / Neuronal migration protein doublecortin, chordata / : / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Doublecortin domain / Neuronal migration protein doublecortin, chordata / : / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MAb 6H10 light chain / Neuronal migration protein doublecortin / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å
AuthorsRuf, A. / Stihle, M. / Benz, J. / Thoma, R. / Rudolph, M.G.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies.
Authors: Burger, D. / Stihle, M. / Sharma, A. / Di Lello, P. / Benz, J. / D'Arcy, B. / Debulpaep, M. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. / Matile, H. / Ross, A. / Rufer, A.C. / Schoch, ...Authors: Burger, D. / Stihle, M. / Sharma, A. / Di Lello, P. / Benz, J. / D'Arcy, B. / Debulpaep, M. / Fry, D. / Huber, W. / Kremer, T. / Laeremans, T. / Matile, H. / Ross, A. / Rufer, A.C. / Schoch, G. / Steinmetz, M.O. / Steyaert, J. / Rudolph, M.G. / Thoma, R. / Ruf, A.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAb 6H10 light chain
B: Ighg protein
H: Ighg protein
L: MAb 6H10 light chain
M: Neuronal migration protein doublecortin
N: Neuronal migration protein doublecortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4878
Polymers113,4166
Non-polymers712
Water6,936385
1
A: MAb 6H10 light chain
B: Ighg protein
M: Neuronal migration protein doublecortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7434
Polymers56,7083
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-40 kcal/mol
Surface area23140 Å2
MethodPISA
2
H: Ighg protein
L: MAb 6H10 light chain
N: Neuronal migration protein doublecortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7434
Polymers56,7083
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-44 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.858, 110.399, 75.092
Angle α, β, γ (deg.)90.000, 106.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody MAb 6H10 light chain


Mass: 23509.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U5BC76
#2: Antibody Ighg protein


Mass: 22799.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighg / Production host: Escherichia coli (E. coli) / References: UniProt: Q569X1
#3: Protein Neuronal migration protein doublecortin / Development of the nervous system / Doublin / Lissencephalin-X / Lis-X


Mass: 10398.659 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP Residues 133-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCX, DBCN, LISX / Production host: Escherichia coli (E. coli) / References: UniProt: O43602
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→41.825 Å / Num. obs: 63983 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 37.398 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.33
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.06-2.111.4070.96197.2
2.11-2.171.1561.16199.8
2.17-2.231.1891.15199.1
2.23-2.30.831.73196.2
2.3-2.380.7271.82199.8
2.38-2.460.6292.22199.9
2.46-2.560.5212.73199.7
2.56-2.660.4093.36199.7
2.66-2.780.3224.32199.4
2.78-2.910.2475.51199.2
2.91-3.070.1847.6199.8
3.07-3.260.1439.79199.6
3.26-3.480.10312.64199.3
3.48-3.760.08114.81198.7
3.76-4.120.06418.18199.2
4.12-4.610.0522.28199.6
4.61-5.320.04922.32199.3
5.32-6.510.0521.55199.1
6.51-9.210.04325.16199.1
9.210.03333.26197.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementResolution: 2.06→41.825 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.2653 3227 5.06 %
Rwork0.1978 --
obs0.2011 63800 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.49 Å2 / Biso mean: 41.7865 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 2.06→41.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7921 0 2 385 8308
Biso mean--28.33 37.1 -
Num. residues----1029
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.49840.7565-1.49392.6138-1.50425.6827-0.0625-0.2914-0.188-0.3874-0.2722-0.17680.62630.16720.10630.35980.0411-0.01170.26080.06770.2779-7.9402-6.153613.0134
21.99930.33170.01432.4729-1.13062.95740.0326-0.11450.0286-0.2208-0.2548-0.44880.32480.45490.20350.24210.07450.06040.27190.05930.2634-2.4783.200911.5283
33.10640.6147-1.47063.0716-2.42686.58820.1578-0.20890.150.0815-0.1692-0.1275-0.1867-0.28990.03360.25730.07550.03190.2343-0.01910.2375-8.9061.734217.0086
41.90330.8932-0.4722.389-1.67840.9215-0.0184-0.0212-0.3077-0.42530.02890.12530.2505-0.21250.03920.352-0.0102-0.05820.2641-0.06650.1933-27.2748-7.609712.4114
55.35191.20511.63962.8131-0.15883.3978-0.36930.6884-0.205-0.79980.40610.44990.39780.0212-0.05150.5171-0.1372-0.09550.40530.03770.3336-36.2852-14.877110.3176
66.55340.89252.26453.7982-0.34333.93590.3134-0.0774-1.3530.22480.08850.45480.8063-0.5585-0.34380.6525-0.1839-0.11140.37450.00640.5615-38.9835-22.637917.1373
75.15452.69041.41273.2218-0.81133.70880.1423-0.3691.1103-0.1485-0.00330.45320.1791-0.31510.00780.26330.0218-0.02550.2756-0.07330.4681-21.44618.36363.0278
88.81441.85861.84532.35490.69543.2383-0.34990.34631.1206-1.01160.47060.4516-0.1587-0.810.3010.4741-0.131-0.18610.45480.2680.2871-23.249517.4527-5.1289
97.59711.0155-1.21423.1308-0.01384.7263-0.24470.44240.0802-0.68020.0445-0.19180.41550.0810.11530.30260.05830.01070.2040.01180.1689-10.679112.4939-3.9825
106.34461.5209-1.10731.5063-1.13821.6631-0.31110.37940.4967-0.60440.37170.29780.3204-0.2530.03710.3572-0.0343-0.08260.25730.05790.2574-19.959713.1891-2.6521
111.017-0.2130.74264.4073-4.91196.6861-0.3721-0.05350.1472-0.80730.45240.75730.9083-0.9611-0.88160.454-0.1304-0.03610.48320.20680.4869-47.4608-10.775120.8694
120.9034-0.17660.01514.7297-5.81878.2234-0.19210.14740.3042-0.17160.16160.17140.0446-0.2586-0.27210.2101-0.0376-0.0850.34690.13920.3536-41.1271.219214.9812
132.5915-0.67220.28584.5948-5.03096.80890.12380.32710.0516-0.1297-0.11960.20350.42410.25990.21690.3246-0.0362-0.0580.24340.05550.2666-35.8566-2.007913.847
141.0458-0.4246-0.09642.4094-3.51836.9058-0.10080.24020.5287-0.36830.14560.40520.568-0.0875-0.10040.3323-0.1284-0.11840.24610.08240.247-39.2142-2.339316.1071
151.63540.6521-0.58985.5271-6.92637.8801-0.28980.16190.14340.29521.00460.659-0.3043-1.502-0.87640.35250.04440.04770.5820.17960.537-48.51220.92320.8037
166.4272-0.06391.54212.2181-0.67220.9757-0.0823-0.263-0.11620.01190.14810.17260.0244-0.0823-0.0370.23770.06640.01880.3159-0.0110.2501-26.2111-6.074349.3748
173.38410.427-0.10760.1881-0.2940.738-0.08930.1931-0.2324-0.11130.0620.04440.10440.07470.04080.23080.0593-0.01640.2548-0.0270.2503-30.6187-9.602644.0793
183.1832-1.25260.54694.71151.23311.7819-0.1414-0.2265-1.09420.53940.00130.76090.634-0.08350.09130.4077-0.00270.12210.23080.05820.6286-51.1032-30.413346.3715
191.73392.5466-0.5968.9503-3.10412.71260.00950.2079-0.2029-0.51260.0125-0.00350.55640.1125-0.19660.3360.008-0.02110.331-0.05340.2871-17.1243-28.485536.5916
203.11390.72240.19185.2373-0.44842.37290.094-0.013-0.20030.14950.0172-0.04750.12460.1225-0.1060.17150.0376-0.01430.2803-0.01340.1972-11.3554-22.747543.9723
211.40581.29960.64471.66621.09790.27830.0446-0.0016-0.1859-0.00730.02850.17120.23520.0509-0.02850.27160.03590.01180.30310.01950.3315-19.2013-25.783940.9341
225.5139-1.30691.87462.637-0.52962.47440.1460.3019-0.2105-0.1177-0.27110.38360.1075-0.28980.17310.26750.0046-0.02360.3771-0.19140.5076-48.3783-33.400430.8959
238.1263-3.45764.12846.0468-3.13895.2242-0.1832-0.21250.2520.3013-0.1487-0.1748-0.0761-0.13330.3060.2961-0.0228-0.020.2177-0.09510.3832-37.5884-32.903437.477
245.4894-0.84471.67493.2076-0.83663.23670.08620.5865-0.1742-0.4179-0.38140.33380.2709-0.31140.12120.37020.0363-0.03030.5205-0.25490.5472-52.0909-34.390325.6706
258.25341.2911-1.24252.93270.57252.7645-0.12-0.2377-0.00950.13930.0168-0.07290.09090.0728-0.05860.2970.04080.0150.27950.11860.236918.953619.12220.2162
262.11451.3824-3.37895.2184-0.52627.60470.4658-0.087-0.06770.1372-0.11010.0780.3068-0.38830.12880.28650.04740.04410.54770.12040.37665.773816.34513.2598
278.72710.6781-1.37383.75740.04944.08170.31710.0973-0.3762-0.0819-0.2506-0.67270.07660.4499-0.00420.29970.05460.02730.35120.09990.467325.70116.0493-6.4834
283.49882.5962-3.73454.6927-0.40928.0377-0.34980.4216-1.2404-0.3392-0.5109-0.76930.1103-0.03770.12610.28250.16270.02890.48510.04760.4917.795214.0707-10.4605
292.51111.7377-1.71075.06281.1793.03880.17061.4255-0.8752-0.24160.073-0.01170.0147-0.9420.16270.34930.0677-0.03880.7188-0.10390.58776.524313.1338-8.9379
308.15660.0802-3.12073.69191.30224.98010.62570.93311.5789-0.7552-0.75050.6496-0.5567-0.4652-0.41030.49890.15590.09380.42050.16450.633813.131427.6072-6.8452
317.52690.6971-2.0413.02151.02078.18980.3834-0.32210.8714-0.55890.0639-0.7046-0.79380.0669-0.37520.38690.03640.14750.41690.01220.562923.236626.3014-3.1714
322.1570.6855-1.04254.13080.57292.00590.31430.40810.6334-0.1941-0.34250.41280.0908-0.5366-0.06070.28890.1390.03790.55380.07070.48237.231623.5314-2.9901
337.78610.39970.61072.3369-0.7482.9410.0602-0.58950.36810.164-0.10970.0009-0.09720.06520.02970.17740.03890.00870.1657-0.00280.21399.833-5.544952.4134
342.41032.8612-1.2753.5494-0.645.3005-0.1679-0.3555-0.0544-0.11540.2803-0.06110.2449-0.2938-0.19430.19860.03330.00490.37250.04080.3236-3.354-9.267251.4954
358.76790.8468-0.00874.3611-1.17064.2358-0.0620.0390.4306-0.2673-0.0826-0.1019-0.3119-0.03440.10850.2221-0.0033-0.02780.1744-0.0350.196716.6357-1.586546.3391
362.19891.70611.17032.8064-0.27823.110.11920.25760.504-0.00080.02080.1957-0.2124-0.3233-0.07410.22270.04070.03470.2519-0.00660.29573.1244-0.019842.2996
375.12980.38450.30761.9711-1.20462.57170.0383-0.70140.54950.48380.09470.013-0.9513-0.03990.00150.43770.00430.00860.2664-0.09120.23767.31672.691555.3016
389.1470.4789-0.55523.14690.31865.5461-0.2038-1.17060.16940.49770.0171-0.0697-0.1746-0.4746-0.19140.28090.09950.02930.487-0.04610.3008-4.0329-0.955855.315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 75 )A19 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 90 )A76 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 143 )A91 - 143
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 198 )A144 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 213 )A199 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 12 )B2 - 12
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 25 )B13 - 25
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 64 )B26 - 64
10X-RAY DIFFRACTION10chain 'B' and (resid 65 through 121 )B65 - 121
11X-RAY DIFFRACTION11chain 'B' and (resid 122 through 136 )B122 - 136
12X-RAY DIFFRACTION12chain 'B' and (resid 137 through 157 )B137 - 157
13X-RAY DIFFRACTION13chain 'B' and (resid 158 through 175 )B158 - 175
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 186 )B176 - 186
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 215 )B187 - 215
16X-RAY DIFFRACTION16chain 'H' and (resid 2 through 43 )H2 - 43
17X-RAY DIFFRACTION17chain 'H' and (resid 44 through 136 )H44 - 136
18X-RAY DIFFRACTION18chain 'H' and (resid 137 through 215 )H137 - 215
19X-RAY DIFFRACTION19chain 'L' and (resid 1 through 18 )L1 - 18
20X-RAY DIFFRACTION20chain 'L' and (resid 19 through 75 )L19 - 75
21X-RAY DIFFRACTION21chain 'L' and (resid 76 through 113 )L76 - 113
22X-RAY DIFFRACTION22chain 'L' and (resid 114 through 155 )L114 - 155
23X-RAY DIFFRACTION23chain 'L' and (resid 156 through 174 )L156 - 174
24X-RAY DIFFRACTION24chain 'L' and (resid 175 through 213 )L175 - 213
25X-RAY DIFFRACTION25chain 'M' and (resid 51 through 59 )M51 - 59
26X-RAY DIFFRACTION26chain 'M' and (resid 60 through 67 )M60 - 67
27X-RAY DIFFRACTION27chain 'M' and (resid 68 through 79 )M68 - 79
28X-RAY DIFFRACTION28chain 'M' and (resid 80 through 90 )M80 - 90
29X-RAY DIFFRACTION29chain 'M' and (resid 91 through 102 )M91 - 102
30X-RAY DIFFRACTION30chain 'M' and (resid 103 through 115 )M103 - 115
31X-RAY DIFFRACTION31chain 'M' and (resid 116 through 123 )M116 - 123
32X-RAY DIFFRACTION32chain 'M' and (resid 124 through 139 )M124 - 139
33X-RAY DIFFRACTION33chain 'N' and (resid 51 through 59 )N51 - 59
34X-RAY DIFFRACTION34chain 'N' and (resid 60 through 67 )N60 - 67
35X-RAY DIFFRACTION35chain 'N' and (resid 68 through 79 )N68 - 79
36X-RAY DIFFRACTION36chain 'N' and (resid 80 through 102 )N80 - 102
37X-RAY DIFFRACTION37chain 'N' and (resid 103 through 128 )N103 - 128
38X-RAY DIFFRACTION38chain 'N' and (resid 129 through 140 )N129 - 140

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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

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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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