[English] 日本語
Yorodumi
- PDB-2yps: Crystal structure of the PX domain of human sorting nexin 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yps
TitleCrystal structure of the PX domain of human sorting nexin 3
ComponentsSORTING NEXIN-3
KeywordsPROTEIN TRANSPORT / ENDOSOME
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / phosphatidylinositol-5-phosphate binding / retromer complex ...negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / phosphatidylinositol-5-phosphate binding / retromer complex / host-mediated suppression of symbiont invasion / early phagosome / phosphatidylinositol-3-phosphate binding / endocytic recycling / phosphatidylinositol-4-phosphate binding / regulation of Wnt signaling pathway / phosphatidylinositol-3,5-bisphosphate binding / clathrin-coated vesicle / negative regulation of phagocytosis / response to bacterium / positive regulation of neuron projection development / negative regulation of protein catabolic process / protein transport / early endosome membrane / protein phosphatase binding / early endosome / endosome membrane / Ub-specific processing proteases / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Vertebrate SNX3, 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCanning, P. / Kiyani, W. / Froese, D.S. / Krojer, T. / Strain-Damerell, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of the Px Domain of Human Sorting Nexin 3
Authors: Canning, P. / Froese, D.S. / Krojer, T. / Strain-Damerell, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Yue, W.W.
History
DepositionOct 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SORTING NEXIN-3
B: SORTING NEXIN-3
C: SORTING NEXIN-3
D: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)62,6114
Polymers62,6114
Non-polymers00
Water18010
1
A: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 81.700, 184.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2001-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1206, 0.992, -0.0367), (0.9923, 0.1215, 0.023), (0.0273, -0.0337, -0.9991)-0.4805, -0.015, -46.4175
2given(-0.3643, -0.559, 0.7449), (-0.5625, -0.5054, -0.6543), (0.7422, -0.6573, -0.1303)20.6694, -12.744, -27.2243
3given(-0.4764, -0.4581, -0.7504), (-0.4281, -0.6246, 0.6531), (-0.7679, 0.6324, 0.1015)-14.1557, 17.5823, -21.0993
4given(-0.4935, -0.443, -0.7485), (-0.4611, -0.5965, 0.657), (-0.7375, 0.6693, 0.0901)-14.8249, 18.3765, -20.1743
5given(-0.3843, -0.5469, 0.7438), (-0.5012, -0.553, -0.6656), (0.7753, -0.6286, -0.0616)19.847, -12.3475, -24.4821
6given(-0.151, 0.9884, -0.0146), (0.9881, 0.1513, 0.0262), (0.0281, -0.0105, -0.9995)0.2348, 0.0828, -46.5244

-
Components

#1: Protein
SORTING NEXIN-3 / PROTEIN SDP3


Mass: 15652.799 Da / Num. of mol.: 4 / Fragment: PX DOMAIN, RESIDUES 24-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MGC / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O60493
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE
Crystal growDetails: 3.5M FORMATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.6→51.02 Å / Num. obs: 16601 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CSK

2csk


Resolution: 2.6→51.02 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.64 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25511 836 5 %RANDOM
Rwork0.21092 ---
obs0.21308 15729 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.029 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å20 Å20 Å2
2---1.58 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 10 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193151
X-RAY DIFFRACTIONr_bond_other_d0.0070.022918
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9614270
X-RAY DIFFRACTIONr_angle_other_deg1.17936635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19223.333135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52715485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5671524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213556
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02731
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 64 -
Rwork0.331 1153 -
obs--99.84 %
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)
12.0334-0.4630.3544.05320.59920.1793-0.0463-0.2010.04390.13170.0469-0.0030.0091-0.0382-0.00060.0554-0.02150.10220.13-0.02920.21840.599619.5605-29.1201
21.58390.1906-0.69020.8773-0.44420.89320.0002-0.08920.0926-0.0038-0.0925-0.06680.08630.04130.09230.0324-0.04140.03240.0982-0.0590.199918.99533.258-16.5252
32.48940.9533-1.0551.0951-0.43490.4618-0.04520.3306-0.04160.02490.0455-0.02080.0329-0.1799-0.00030.0722-0.11270.03660.2415-0.01010.0837-12.0235-3.3839-35.1579
41.56811.0415-0.09931.60130.31090.7111-0.0205-0.06120.01160.15390.0733-0.04940.1524-0.1169-0.05270.1609-0.0780.02760.1162-0.02050.0738-1.3505-12.9242-11.2757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 148
2X-RAY DIFFRACTION2B27 - 148
3X-RAY DIFFRACTION3C27 - 147
4X-RAY DIFFRACTION4D27 - 150

+
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