[English] 日本語
Yorodumi
- PDB-4pqp: Crystal structure of human SNX14 PX domain in space group P43212 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pqp
TitleCrystal structure of human SNX14 PX domain in space group P43212
ComponentsSorting nexin-14
KeywordsPROTEIN TRANSPORT / sorting nexin / phox homology domain / phosphoinositide binding
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane ...phosphatidylinositol-3,5-bisphosphate binding / postsynaptic modulation of chemical synaptic transmission / autophagosome maturation / phosphatidylinositol binding / protein transport / late endosome / late endosome membrane / postsynapse / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / dendrite / cytosol
Similarity search - Function
Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain ...Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain / RGS, subdomain 2 / PX domain profile. / PX domain / Phox homology / PX domain superfamily / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMas, C. / Norwood, S. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Teasdale, R. / Collins, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling.
Authors: Mas, C. / Norwood, S.J. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Ghai, R. / Ona Yanez, L.E. / Davis, J.L. / Teasdale, R.D. / Collins, B.M.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting nexin-14
B: Sorting nexin-14
C: Sorting nexin-14
D: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0936
Polymers60,9094
Non-polymers1842
Water34219
1
A: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3192
Polymers15,2271
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sorting nexin-14


Theoretical massNumber of molelcules
Total (without water)15,2271
Polymers15,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3192
Polymers15,2271
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sorting nexin-14


Theoretical massNumber of molelcules
Total (without water)15,2271
Polymers15,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.670, 121.670, 82.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
21chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
31chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
41chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A563 - 575
121chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A608 - 644
131chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A649 - 686
211chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B563 - 575
221chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B608 - 644
231chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B649 - 686
311chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C563 - 575
321chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C608 - 644
331chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C649 - 686
411chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D563 - 575
421chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D608 - 644
431chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D649 - 686

-
Components

#1: Protein
Sorting nexin-14 / SNX14


Mass: 15227.159 Da / Num. of mol.: 4 / Fragment: PX domain (UNP residues 561-686)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5W7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.1 M sodium citrate tribasic, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→68.2 Å / Num. all: 12933 / Num. obs: 12933 / % possible obs: 100 % / Observed criterion σ(I): 4.7 / Redundancy: 27.8 % / Biso Wilson estimate: 89.5 Å2 / Rmerge(I) obs: 0.14
Reflection shellHighest resolution: 3 Å

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.948 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 629 4.88 %RANDOM
Rwork0.2343 ---
obs0.2368 12883 99.95 %-
all-12883 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 12 19 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113563
X-RAY DIFFRACTIONf_angle_d1.4524818
X-RAY DIFFRACTIONf_dihedral_angle_d18.7441317
X-RAY DIFFRACTIONf_chiral_restr0.121494
X-RAY DIFFRACTIONf_plane_restr0.007611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A748X-RAY DIFFRACTIONPOSITIONAL0.079
12B748X-RAY DIFFRACTIONPOSITIONAL0.079
13C748X-RAY DIFFRACTIONPOSITIONAL0.082
14D714X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30190.33131670.27632982X-RAY DIFFRACTION100
3.3019-3.77960.30961460.24023027X-RAY DIFFRACTION100
3.7796-4.76120.26581540.20863046X-RAY DIFFRACTION100
4.7612-48.95450.27691620.23983199X-RAY DIFFRACTION100
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)
19.9932-6.21460.4499.842-3.17997.9333-0.3643-1.1484-0.90210.16580.37180.12740.18040.48980.01730.6574-0.0187-0.06270.50830.09610.4822132.4762-33.272797.4746
24.97422.3148-2.87127.0084-1.86719.75650.0886-0.23680.73630.8053-0.037-0.2228-0.7939-0.4119-0.12010.58770.0804-0.10220.5335-0.10770.4678130.9221-25.163290.7785
34.76883.3335-1.02812.0102-7.83286.42131.41993.8653-2.2827-0.0451-3.1445-2.932-1.05522.3930.69781.3841.0804-0.56382.30610.08651.0732145.0649-34.668986.4862
410.1652.5363-4.13693.6969-0.79333.1413-0.4064-1.15-0.05471.40670.19160.0956-0.6006-0.24130.26060.87590.1252-0.07950.6757-0.1470.6272132.1924-24.185794.1685
56.88376.2241-2.18537.4902-1.49635.7929-0.4783-1.22970.4589-0.09880.31270.4308-1.89670.0387-0.05511.43940.0441-0.08120.5213-0.10440.6599149.0715-8.475381.0633
64.8153-1.5476-1.5673.48620.83763.66930.9471-1.2079-0.65542.8503-1.02720.4417-0.01760.2036-0.07621.4698-0.1304-0.01870.58360.10290.5972152.2991-4.352584.0642
76.41231.7558-3.43486.78240.97555.36860.4326-0.3591-0.02590.47-0.2271-0.0085-0.77450.734-0.20530.7926-0.0024-0.10460.5120.05590.498153.9188-12.829774.0452
86.2567-5.22574.2939.493-0.10995.3637-0.5985-0.1942-0.45180.66520.39590.8966-1.30650.27970.31971.48480.13680.23830.59520.11050.5925147.9502-45.713463.0334
95.7876-2.17330.99232.46230.23822.6230.77540.5295-0.4903-2.502-1.41150.28920.05610.66610.46931.47580.02140.19090.71730.21350.7954152.3677-51.380159.9207
106.829-2.22281.13547.34020.64336.0963-0.4908-0.15110.3928-0.63530.1801-0.31470.03910.50320.29030.6528-0.08240.10050.53980.06930.6668151.2335-39.744971.3215
118.47522.8665-2.70799.8781.99354.39370.1695-0.2347-0.8880.4450.0502-1.09791.61132.3586-0.29990.86930.32450.19760.88450.06170.9425158.2282-50.876371.9847
129.82245.6114-3.24333.94110.22285.1458-0.4191-0.18670.6238-2.12770.27070.51850.0812-0.2796-0.02690.88560.0196-0.24850.57650.10390.6759167.4454-30.644687.0583
133.76273.9449-3.17515.3655-0.54456.0168-0.68371.8191.1324-0.20210.74610.8721-0.4673-1.72760.11580.7731-0.1981-0.32481.440.27940.8193170.6713-28.998485.618
147.98041.8046-2.5974.5679-0.53225.16050.04820.43920.5171-0.57440.14151.0924-0.2205-0.3771-0.12670.730.2312-0.16770.87760.10630.7343167.0267-27.534696.9178
155.7054-5.9469-4.25969.84871.14666.17720.5427-0.1381-0.6385-0.8887-0.22450.9777-1.2339-0.4708-0.22230.66430.0965-0.09950.8017-0.02240.8706164.836-22.171793.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 563 through 590 )
2X-RAY DIFFRACTION2chain 'A' and (resid 591 through 641 )
3X-RAY DIFFRACTION3chain 'A' and (resid 642 through 649 )
4X-RAY DIFFRACTION4chain 'A' and (resid 650 through 686 )
5X-RAY DIFFRACTION5chain 'B' and (resid 562 through 587 )
6X-RAY DIFFRACTION6chain 'B' and (resid 588 through 609 )
7X-RAY DIFFRACTION7chain 'B' and (resid 610 through 686 )
8X-RAY DIFFRACTION8chain 'C' and (resid 563 through 587 )
9X-RAY DIFFRACTION9chain 'C' and (resid 588 through 610 )
10X-RAY DIFFRACTION10chain 'C' and (resid 611 through 668 )
11X-RAY DIFFRACTION11chain 'C' and (resid 669 through 686 )
12X-RAY DIFFRACTION12chain 'D' and (resid 562 through 577 )
13X-RAY DIFFRACTION13chain 'D' and (resid 586 through 609 )
14X-RAY DIFFRACTION14chain 'D' and (resid 610 through 630 )
15X-RAY DIFFRACTION15chain 'D' and (resid 631 through 686 )

+
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