[English] 日本語
Yorodumi
- PDB-4akv: Crystal structure of human sorting nexin 33 (SNX33) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4akv
TitleCrystal structure of human sorting nexin 33 (SNX33)
ComponentsSORTING NEXIN-33
KeywordsTRANSPORT PROTEIN / ORGANELLE BIOGENESIS
Function / homology
Function and homology information


plasma membrane tubulation / macropinocytosis / cleavage furrow formation / negative regulation of protein localization to cell surface / positive regulation of protein localization to cell surface / endosome organization / negative regulation of endocytosis / protein import / endosomal transport / positive regulation of membrane protein ectodomain proteolysis ...plasma membrane tubulation / macropinocytosis / cleavage furrow formation / negative regulation of protein localization to cell surface / positive regulation of protein localization to cell surface / endosome organization / negative regulation of endocytosis / protein import / endosomal transport / positive regulation of membrane protein ectodomain proteolysis / mitotic cytokinesis / extrinsic component of membrane / phosphatidylinositol binding / intracellular protein transport / cytoplasmic vesicle membrane / endocytosis / cytoplasmic vesicle / membrane / identical protein binding / cytosol
Similarity search - Function
Sorting nexin-33, BAR domain / Sorting nexin-33 / WASP-binding domain of Sorting nexin protein / Sorting nexin protein, WASP-binding domain / Sorting nexin 9 family / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Sorting nexin-33, BAR domain / Sorting nexin-33 / WASP-binding domain of Sorting nexin protein / Sorting nexin protein, WASP-binding domain / Sorting nexin 9 family / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.651 Å
AuthorsOberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Oberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Structure of Human Sorting Nexin 33
Authors: Oberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SORTING NEXIN-33
B: SORTING NEXIN-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3268
Polymers90,7492
Non-polymers5766
Water1,11762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-132 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)68.650, 216.210, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein SORTING NEXIN-33 / / SORTING NEXIN 33 / SH3 AND PX DOMAIN-CONTAINING PROTEIN 3


Mass: 45374.742 Da / Num. of mol.: 2 / Fragment: PH-BAR DOMAIN, RESIDUES 212-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8WV41
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.38 Å3/Da / Density % sol: 48.31 % / Description: NONE

-
Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→216.14 Å / Num. obs: 25956 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 72.32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.651→65.431 Å / SU ML: 0.5 / σ(F): 1.37 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 1318 5.1 %
Rwork0.2105 --
obs0.2134 25895 99.68 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.597 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.396 Å20 Å20 Å2
2--4.1052 Å20 Å2
3---6.2908 Å2
Refinement stepCycle: LAST / Resolution: 2.651→65.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 30 62 5805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025877
X-RAY DIFFRACTIONf_angle_d0.6147902
X-RAY DIFFRACTIONf_dihedral_angle_d11.852215
X-RAY DIFFRACTIONf_chiral_restr0.047808
X-RAY DIFFRACTIONf_plane_restr0.0031025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6513-2.75740.4021250.34912632X-RAY DIFFRACTION98
2.7574-2.88290.40471550.3092662X-RAY DIFFRACTION100
2.8829-3.03490.37371460.292689X-RAY DIFFRACTION100
3.0349-3.22510.34261500.25892711X-RAY DIFFRACTION100
3.2251-3.47410.29081540.24692701X-RAY DIFFRACTION100
3.4741-3.82360.28391460.21532713X-RAY DIFFRACTION100
3.8236-4.37680.23241600.17942728X-RAY DIFFRACTION100
4.3768-5.51390.22681330.16842794X-RAY DIFFRACTION100
5.5139-65.45080.24251490.19922947X-RAY DIFFRACTION100
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)
13.8045-0.23651.78272.68141.38336.21230.1649-0.6459-0.21860.7593-0.09560.1323-0.515-1.076-0.06610.96380.02120.13980.67860.05810.6043-13.5948-41.6518-20.6322
24.34010.52011.16773.96530.23073.45670.2842-0.4393-0.89410.7613-0.0316-0.25250.718-0.0429-0.28680.76130.073-0.03160.49320.07310.6622-6.2917-48.6943-21.6383
32.00783.66692.41767.0174.32793.51480.0510.3092-0.28530.28030.4069-0.52450.39720.5586-0.4830.44940.09180.01010.5382-0.02440.52319.68-23.9135-25.7457
41.77332.17421.61346.1673.72772.913-0.011-0.04210.33820.3118-0.41891.10430.37910.02930.44140.47680.01810.0360.4760.0960.4697-3.2419-31.4744-32.2554
53.19030.12620.36933.12291.86097.0031-0.18320.26930.2792-0.4387-0.084-0.0928-0.97240.13650.27130.4622-0.0294-0.07750.48890.05260.472430.5127.033-26.1562
69.044-1.3539-4.79276.14043.59093.936-0.21040.05-0.08230.7321-0.172-0.0623-0.22371.30170.38451.048-0.1655-0.25450.92750.1790.69136.513133.1202-4.5215
72.94663.43882.1564.79832.70812.5858-0.14060.4378-0.1379-0.05040.3663-0.31150.07210.5171-0.23190.3670.03270.04270.55410.00410.523821.2203-1.6837-22.7471
81.80522.52171.70865.10732.32833.0047-0.23720.00410.45030.06750.02270.4076-0.33720.34010.23010.44350.01680.04330.6149-0.00770.449426.243614.1901-11.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 211:265)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 266:371)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 372:502)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 503:573)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 207:350)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 351:369)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 370:496)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 497:573)

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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