[English] 日本語
Yorodumi
- PDB-5gw1: Crystal structure of SNX16 PX-Coiled coil in space group P212121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gw1
TitleCrystal structure of SNX16 PX-Coiled coil in space group P212121
ComponentsSorting nexin-16
KeywordsPROTEIN TRANSPORT / Sortin nexin / PX domain / Endosome sorting
Function / homology
Function and homology information


extrinsic component of endosome membrane / protein targeting to lysosome / early endosome to late endosome transport / endosome to lysosome transport / phosphatidylinositol binding / late endosome / late endosome membrane / early endosome membrane / lysosome / early endosome ...extrinsic component of endosome membrane / protein targeting to lysosome / early endosome to late endosome transport / endosome to lysosome transport / phosphatidylinositol binding / late endosome / late endosome membrane / early endosome membrane / lysosome / early endosome / intracellular membrane-bounded organelle / identical protein binding / cytosol
Similarity search - Function
SNX16, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.35 Å
AuthorsXu, J. / Liu, J.
CitationJournal: Structure / Year: 2017
Title: SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding.
Authors: Xu, J. / Zhang, L. / Ye, Y. / Shan, Y. / Wan, C. / Wang, J. / Pei, D. / Shu, X. / Liu, J.
History
DepositionSep 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting nexin-16
B: Sorting nexin-16
C: Sorting nexin-16
D: Sorting nexin-16
E: Sorting nexin-16
F: Sorting nexin-16
G: Sorting nexin-16
H: Sorting nexin-16


Theoretical massNumber of molelcules
Total (without water)171,6098
Polymers171,6098
Non-polymers00
Water0
1
A: Sorting nexin-16
B: Sorting nexin-16


Theoretical massNumber of molelcules
Total (without water)42,9022
Polymers42,9022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-38 kcal/mol
Surface area22120 Å2
MethodPISA
2
C: Sorting nexin-16
D: Sorting nexin-16


Theoretical massNumber of molelcules
Total (without water)42,9022
Polymers42,9022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-29 kcal/mol
Surface area22430 Å2
MethodPISA
3
E: Sorting nexin-16
F: Sorting nexin-16


Theoretical massNumber of molelcules
Total (without water)42,9022
Polymers42,9022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area23350 Å2
MethodPISA
4
G: Sorting nexin-16
H: Sorting nexin-16


Theoretical massNumber of molelcules
Total (without water)42,9022
Polymers42,9022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-29 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.670, 133.060, 215.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Sorting nexin-16 /


Mass: 21451.066 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 100-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P57768

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.32 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 31mM Citric, 69mM Bis-tris Propanol, 18% PEG 5000, 70mM NaF, 2mM TCEP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.35→61.91 Å / Num. obs: 32016 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 106.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.053 / Rrim(I) all: 0.112 / Net I/σ(I): 13.8 / Num. measured all: 139054 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.35-3.534.50.7042058546050.6830.3710.7992.599.9
10.59-61.9140.057427010810.9860.0320.06643.396.2

-
Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
Aimlessdata reduction
MOLREPphasing
RefinementResolution: 3.35→19.995 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 31.23
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2863 2960 4.95 %
Rwork0.2572 --
obs0.2586 31948 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 248.02 Å2 / Biso mean: 87.54 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: final / Resolution: 3.35→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11563 0 0 0 11563
Num. residues----1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811801
X-RAY DIFFRACTIONf_angle_d1.46815890
X-RAY DIFFRACTIONf_chiral_restr0.0811724
X-RAY DIFFRACTIONf_plane_restr0.0062051
X-RAY DIFFRACTIONf_dihedral_angle_d16.8964618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3501-3.40470.44051330.346927792912100
3.4047-3.46310.36961450.355327072852100
3.4631-3.52580.35291530.3326582811100
3.5258-3.59320.31241750.31522707288299
3.5932-3.66610.32581310.294427142845100
3.6661-3.74530.3191580.303726902848100
3.7453-3.83190.37711310.29872723285499
3.8319-3.9270.30071590.300527082867100
3.927-4.03230.30361240.27827332857100
4.0323-4.14990.32581280.2782712284099
4.1499-4.28260.28281240.269527072831100
4.2826-4.43410.27611450.26422700284599
4.4341-4.60960.30611570.25282700285799
4.6096-4.81660.30111310.24752704283599
4.8166-5.06660.27891580.24312709286799
5.0666-5.37820.30871580.26542672283099
5.3782-5.78410.31021400.28262652279298
5.7841-6.34920.34381280.28782677280598
6.3492-7.22970.27581350.261927012836100
7.2297-8.96970.24321130.227127572870100
8.9697-19.9950.19151340.17672686282099
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)
10.47730.03250.01661.8122-0.57011.2577-0.00540.02290.0474-0.70170.2372-0.4677-0.05730.5025-0.53390.61260.04950.1420.6499-0.56790.2594-21.27348.216749.3881
21.49540.14490.42480.77920.30480.76120.49860.3285-0.4009-0.33770.0382-0.10490.43530.24550.49160.32750.00390.14920.0449-0.7505-0.4771-24.19743.390344.0865
31.05190.40450.16461.3675-1.04373.64240.29850.19870.5624-0.28790.6408-0.4066-0.670.26497.09360.3455-0.07420.1980.1664-0.904-0.2032-23.83256.222544.6861
40.7290.48880.81590.43420.52530.7446-0.15891.0106-0.1015-0.4103-0.0318-0.29250.03640.6009-0.06861.1261-0.0597-0.12060.8983-0.2830.8581-34.07492.3128.4223
50.4401-0.2545-0.20670.3171-0.17570.59490.29530.11920.2238-0.3576-0.17190.619-1.7792-0.36820.00562.1643-0.51960.33331.3325-0.35841.2893-8.222334.118620.9456
62.9611-0.11020.05490.00610.00420.0047-0.49180.6970.804-0.74370.1614-0.0968-1.1145-0.0476-0.06212.4315-0.35780.27150.68050.04010.8482-9.865538.226819.5017
70.6888-0.00190.02220.1178-0.12960.61510.1930.3738-0.0475-0.3533-0.16260.4058-0.7772-0.40651.06921.84950.10120.19680.6603-0.14910.8726-20.63126.63112.789
81.75840.55-1.2950.7687-0.31810.98320.4297-0.59620.2327-0.4783-0.3406-0.0484-1.9740.440.00851.9741-0.36840.06440.7342-0.1310.9561-12.718330.511515.7299
90.53360.27530.15210.18470.22750.21340.254-0.3170.37910.4354-0.38060.43990.5465-1.0416-0.0020.9965-0.1173-0.09750.8343-0.00860.6291-38.15653.27814.4392
107.07680.55611.41540.05-0.00942.86240.47970.29272.0150.42720.12270.5257-2.116-0.5977-0.48691.44350.19510.28541.38950.47030.9637-43.105989.778743.3803
112.466-0.70270.30421.6242-1.00292.88810.36320.5501-0.2424-0.19180.1811-0.60310.7615-0.32630.06670.3196-0.0502-0.09010.18230.2454-0.0329-44.393771.855536.9312
124.35952.1261-1.09391.0366-0.53380.2739-0.2541-0.9329-1.60530.053-0.9966-0.56970.9035-0.0285-0.37061.90990.3229-0.24540.838-0.05821.0482-35.878955.748334.6648
132.390.788-1.41811.4731-0.02733.01170.32050.3451-0.2666-0.30910.16610.14190.5987-0.48620.2170.2962-0.01120.0830.59320.27040.1353-45.520874.97937.4275
140.17630.0068-0.14410.1448-0.25030.3793-0.50810.7827-1.4472-0.4086-0.2719-0.01510.5966-0.7901-0.01051.1777-0.31210.10581.2163-0.02160.8007-34.24566.1890.8735
152.37940.97290.340.4379-0.03370.7511-0.23150.1414-0.0962-0.0519-0.5043-0.11350.6525-0.3922-4.84392.388-1.36340.1781.83920.01320.9304-61.615833.704816.3124
161.9484-0.93351.31910.5067-0.60411.1110.685-0.7803-0.0541-0.0579-0.73520.05580.58590.73330.4322.5399-0.54790.33171.53180.0070.781-59.853640.540924.3468
171.52731.0727-1.62721.2999-2.62156.9754-0.5594-0.0483-0.93140.425-0.3087-0.35751.42660.4485-0.40051.7805-0.6647-0.02451.0126-0.08030.991-51.175341.649515.2269
181.1529-0.70731.24341.38610.09652.12151.33860.39120.2323-0.8280.206-0.03181.35370.13690.25781.3602-0.111-0.05860.68320.00670.9819-53.005543.76843.8474
190.0123-0.0110.00130.04010.03450.03680.71340.11010.01240.16210.2141.3311-0.39-0.56080.00022.6661-0.1294-0.2911.8384-0.06491.8331-62.823856.138815.6085
202.4211-0.884-1.05880.69980.38810.46920.516-0.42170.1714-0.0979-0.74130.1462-0.0937-0.82780.38321.9468-0.3592-0.42421.2838-0.17510.6979-62.11140.853310.5681
210.25240.24610.13250.23380.12890.06660.9676-0.5131-0.76890.9908-1.1760.47431.1928-0.5658-0.00582.2602-0.1806-0.23451.1878-0.21571.3994-49.507431.242818.9441
220.73480.0676-0.09090.04360.15410.461-0.02790.1063-0.86130.69460.1971-0.61230.037-0.24720.00661.4961-0.15580.33151.1297-0.0840.7613-34.314361.319411.9081
230.0727-0.0164-0.02520.00610.01490.0527-0.73350.0870.2569-0.1833-0.3922-0.0479-0.2517-0.2885-0.00361.077-0.04790.01520.9114-0.32680.8102-15.146284.7469-14.3338
240.04430.46070.05734.27070.64090.08110.55311.1606-0.2704-1.54830.1098-0.03310.88152.28590.40261.22690.8110.15932.4235-0.00671.0661-58.076393.60912.5514
250.0663-0.3564-0.15032.00431.01710.89930.35371.1947-0.07371.45060.0035-0.72811.81621.17330.01561.62420.7276-0.05331.9867-0.16221.5901-58.90982.395920.0417
264.99372.54152.15662.60631.55731.4149-0.64522.0690.3042-1.1874-0.7114-1.0643-0.64440.9828-0.54141.51850.8210.09312.14630.22411.199-65.00289.15576.5957
27-0.00420.1274-0.03590.1908-0.06960.01360.6835-0.4706-0.19320.6375-0.2180.76371.212-0.2747-0.00022.3949-0.0652-0.04551.30680.22391.691-84.733362.291131.5867
284.5241-0.13181.23294.5353-0.62312.50180.04680.2260.11270.34270.1735-0.01230.41890.11060.0573-0.19630.06180.10580.1741-0.0380.0785-95.76295.493228.3441
29-0.08540.01-0.0141-0.0111-0.0459-0.05410.2239-0.5176-0.65370.2753-0.3412-2.11591.4926-0.29610.00942.1316-0.159-0.02040.890.38292.3697-77.49662.265535.3476
300.9941-0.1354-0.27550.6711-0.2491.16740.877-1.7683-1.13640.9354-0.1502-0.51150.0835-1.32790.00720.6971-0.1024-0.16560.94710.12691.0605-46.8344107.8641.7799
312.7644-0.3429-0.35523.27530.43392.03710.1016-0.6442-0.96230.2520.00760.46270.5527-0.5448-0.00770.2915-0.0545-0.20610.8977-0.07690.7679-46.6504115.102142.6498
32-0.0423-0.03260.04260.1297-0.26550.61620.1229-0.68831.3954-0.31230.48150.3771-1.33930.80960.38762.0155-0.51190.12961.2717-0.50462.4516-64.929147.120342.227
335.4157-1.054-0.34892.7115-0.07550.03970.37290.72490.6515-0.9553-0.02090.20560.05590.27630.09950.6926-0.26130.2880.4952-0.36860.7442-85.7695116.767825.4672
341.64390.6571-1.20521.7341-0.28162.04870.06640.84550.4467-0.1272-0.03470.2127-0.67940.09480.01260.38490.09410.00370.3476-0.02240.7395-80.7795123.491625.6317
351.15110.53980.69160.42610.23150.46871.3412-0.5878-0.51550.65790.7967-1.43210.38170.42140.04641.4739-0.1498-0.14981.1924-0.11571.1618-78.0098118.855743.7471
361.2633-0.17720.6030.69390.82191.5491-0.66980.06621.3229-0.4904-0.25480.0547-0.3821-0.2858-2.45260.78720.0694-0.12940.125-0.33260.7342-83.4299122.889223.0042
370.44470.51510.40630.48410.40260.32280.8193-0.27750.45710.85680.2985-1.1675-0.90690.5110.03641.6877-0.34590.37521.2615-0.30511.7961-58.8506143.600337.8098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 122 )A104 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 168 )A123 - 168
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 232 )A169 - 232
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 278 )A233 - 278
5X-RAY DIFFRACTION5chain 'B' and (resid 105 through 122 )B105 - 122
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 145 )B123 - 145
7X-RAY DIFFRACTION7chain 'B' and (resid 146 through 158 )B146 - 158
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 232 )B159 - 232
9X-RAY DIFFRACTION9chain 'B' and (resid 233 through 277 )B233 - 277
10X-RAY DIFFRACTION10chain 'E' and (resid 103 through 110 )E103 - 110
11X-RAY DIFFRACTION11chain 'E' and (resid 111 through 168 )E111 - 168
12X-RAY DIFFRACTION12chain 'E' and (resid 169 through 177 )E169 - 177
13X-RAY DIFFRACTION13chain 'E' and (resid 178 through 232 )E178 - 232
14X-RAY DIFFRACTION14chain 'E' and (resid 233 through 278 )E233 - 278
15X-RAY DIFFRACTION15chain 'F' and (resid 105 through 117 )F105 - 117
16X-RAY DIFFRACTION16chain 'F' and (resid 118 through 138 )F118 - 138
17X-RAY DIFFRACTION17chain 'F' and (resid 139 through 158 )F139 - 158
18X-RAY DIFFRACTION18chain 'F' and (resid 159 through 168 )F159 - 168
19X-RAY DIFFRACTION19chain 'F' and (resid 169 through 180 )F169 - 180
20X-RAY DIFFRACTION20chain 'F' and (resid 181 through 197 )F181 - 197
21X-RAY DIFFRACTION21chain 'F' and (resid 198 through 224 )F198 - 224
22X-RAY DIFFRACTION22chain 'F' and (resid 225 through 272 )F225 - 272
23X-RAY DIFFRACTION23chain 'F' and (resid 273 through 278 )F273 - 278
24X-RAY DIFFRACTION24chain 'G' and (resid 109 through 140 )G109 - 140
25X-RAY DIFFRACTION25chain 'G' and (resid 141 through 206 )G141 - 206
26X-RAY DIFFRACTION26chain 'G' and (resid 207 through 232 )G207 - 232
27X-RAY DIFFRACTION27chain 'G' and (resid 233 through 277 )G233 - 277
28X-RAY DIFFRACTION28chain 'H' and (resid 106 through 232 )H106 - 232
29X-RAY DIFFRACTION29chain 'H' and (resid 233 through 278 )H233 - 278
30X-RAY DIFFRACTION30chain 'C' and (resid 103 through 131 )C103 - 131
31X-RAY DIFFRACTION31chain 'C' and (resid 132 through 232 )C132 - 232
32X-RAY DIFFRACTION32chain 'C' and (resid 233 through 278 )C233 - 278
33X-RAY DIFFRACTION33chain 'D' and (resid 106 through 119 )D106 - 119
34X-RAY DIFFRACTION34chain 'D' and (resid 120 through 168 )D120 - 168
35X-RAY DIFFRACTION35chain 'D' and (resid 169 through 177 )D169 - 177
36X-RAY DIFFRACTION36chain 'D' and (resid 178 through 227 )D178 - 227
37X-RAY DIFFRACTION37chain 'D' and (resid 228 through 277 )D228 - 277

+
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://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