[English] 日本語
Yorodumi
- PDB-4n5c: Crystal structure of Ypp1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n5c
TitleCrystal structure of Ypp1
ComponentsCargo-transport protein YPP1
KeywordsPROTEIN BINDING / HEAT-like repeat / component of Stt4 complex / Efr3 / Stt4 / Plasma membrane
Function / homology
Function and homology information


response to pheromone / actin cortical patch / protein targeting to vacuole / receptor-mediated endocytosis / protein localization to plasma membrane / endosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Cargo-transport protein YPP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement_SAD / Resolution: 3.25 Å
AuthorsWu, X. / Chi, R.J. / Baskin, J.M. / Lucast, L. / Burd, C.G. / De Camilli, P. / Reinisch, K.M.
CitationJournal: Dev.Cell / Year: 2014
Title: Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex.
Authors: Wu, X. / Chi, R.J. / Baskin, J.M. / Lucast, L. / Burd, C.G. / De Camilli, P. / Reinisch, K.M.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cargo-transport protein YPP1
B: Cargo-transport protein YPP1
C: Cargo-transport protein YPP1
D: Cargo-transport protein YPP1
E: Cargo-transport protein YPP1
F: Cargo-transport protein YPP1
G: Cargo-transport protein YPP1
H: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)755,5158
Polymers755,5158
Non-polymers00
Water00
1
A: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cargo-transport protein YPP1


Theoretical massNumber of molelcules
Total (without water)94,4391
Polymers94,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.545, 136.650, 154.125
Angle α, β, γ (deg.)76.69, 85.67, 72.74
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Cargo-transport protein YPP1 / Alpha-synuclein protective protein 1


Mass: 94439.352 Da / Num. of mol.: 8 / Fragment: residues 11-731 and 742-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YPP1, YGR198W, G7594 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46951

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 Bis-Tris propane [pH 7.5], 0.2 M sodium bromide, 19% PEG 3,350, and 20 mM taurine, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.25→25 Å / Num. all: 114807 / Num. obs: 114807 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 2 % / Rmerge(I) obs: 0.112
Reflection shellResolution: 3.25→3.37 Å / Rmerge(I) obs: 0.582 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement_SAD / Resolution: 3.25→25 Å / SU ML: 0.47 / σ(F): 1.96 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 1970 1.72 %Thin shell selection
Rwork0.2398 ---
obs0.2404 105216 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48674 0 0 0 48674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00449709
X-RAY DIFFRACTIONf_angle_d0.94467178
X-RAY DIFFRACTIONf_dihedral_angle_d13.30718353
X-RAY DIFFRACTIONf_chiral_restr0.047465
X-RAY DIFFRACTIONf_plane_restr0.0058481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.33110.33961000.32098102X-RAY DIFFRACTION99
3.3311-3.42090.37851950.31297972X-RAY DIFFRACTION99
3.4209-3.52140.3656990.30938067X-RAY DIFFRACTION98
3.5214-3.63470.33781960.29618017X-RAY DIFFRACTION99
3.6347-3.76420.3072990.27678123X-RAY DIFFRACTION99
3.7642-3.91440.30471980.26567961X-RAY DIFFRACTION99
3.9144-4.09180.3022980.2498114X-RAY DIFFRACTION99
4.0918-4.30650.2528990.2338129X-RAY DIFFRACTION99
4.3065-4.57480.26651970.20947991X-RAY DIFFRACTION99
4.5748-4.92560.2578970.20848138X-RAY DIFFRACTION99
4.9256-5.41680.27781990.22998013X-RAY DIFFRACTION99
5.4168-6.19030.34071000.26048117X-RAY DIFFRACTION99
6.1903-7.76080.24711980.23837994X-RAY DIFFRACTION99
7.7608-25.11820.1837950.18517985X-RAY DIFFRACTION97
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)
13.96770.8742-2.18983.4777-1.17163.0495-0.1235-0.5967-0.73850.4393-0.16270.22410.3199-0.05530.18930.33610.10880.05420.41440.19090.653621.812654.419187.0414
20.872-0.1205-0.17435.7720.02660.72320.1522-0.1312-0.0140.0775-0.17540.3136-0.04360.04870.01810.2290.1058-0.05580.386-0.03010.257622.820683.840374.3089
31.64470.2189-0.94431.62890.17174.08190.13470.18690.3287-0.1761-0.2165-0.3897-0.25310.6340.05390.43680.07540.07790.59380.08970.464936.8377100.563860.9598
45.0751-0.739-0.50322.5031-0.52551.1537-0.0701-0.1456-0.29950.47240.05870.4151-0.0359-0.03570.03780.6795-0.02270.23430.2342-0.05570.281550.2186-9.397288.5732
52.93681.193-0.8895.0104-0.01511.29890.0412-0.15740.91230.26630.08310.54030.17880.0145-0.10840.4575-0.05850.05890.3319-0.08350.521152.229618.502672.7495
63.97330.2127-1.29611.23660.3313.666-0.11380.23881.1675-0.08850.14940.0343-0.4032-0.2302-0.01470.3772-0.01840.01530.26470.07820.839266.701534.155258.4248
73.09561.3939-0.45283.534-0.04041.0146-0.17480.28260.1383-0.68930.1373-0.4665-0.11140.22770.02030.5530.04370.18720.36290.06220.39049.219710.009102.7224
83.6123-2.60980.47913.7205-0.26660.1958-0.18750.03780.2196-0.17160.0342-0.1952-0.0023-0.01250.11560.37570.0132-0.00940.2965-0.03040.2126-12.132328.3342116.6175
92.6041-0.02070.21790.9313-0.82913.0404-0.0616-0.478-0.08930.39520.06460.38730.357-0.1982-0.00590.69290.02980.1360.47880.00610.5214-33.655728.9564130.1818
102.75761.3044-0.30023.8646-0.02712.24120.05960.17010.2628-0.25670.0768-0.4277-0.11230.2499-0.1340.24240.13480.04290.32590.02760.447177.247774.9329100.9242
114.4254-2.7347-0.4482.81560.14310.0744-0.160.00180.21890.12260.0522-0.25310.10650.20130.05890.32670.0377-0.00770.3558-0.03530.213756.172392.8663116.3331
123.56870.1063-0.52311.5274-1.41484.55830.127-0.3080.06810.20250.17260.37890.0507-0.0007-0.28790.402-0.02650.07680.3204-0.02870.363434.028392.5383129.4186
133.04570.086-0.78832.6731-0.30932.7512-0.17360.08260.1385-0.18820.2724-0.0723-0.08690.1842-0.07890.2702-0.0494-0.06810.14680.07730.516614.733160.415937.3981
141.72660.5968-0.79213.3422-1.28922.1638-0.14470.16230.0693-0.23120.154-0.15250.52630.1053-0.00040.4475-0.0102-0.13450.244-0.07830.341810.319329.770436.4651
154.40470.4531-0.12321.0480.37241.55-0.2297-0.0282-0.74920.0490.30550.25980.9192-0.4109-0.02610.7423-0.1898-0.00960.41340.04940.5572-6.143613.45745.0894
163.893-0.5420.08252.46211.00712.7156-0.44780.08670.16850.01830.4594-0.421-0.61650.3825-0.01520.5729-0.08380.0790.2744-0.10890.382645.5913-5.500438.8311
172.7382-0.8293-0.09815.0231-1.68192.0479-0.0925-0.2702-0.34830.31180.19470.0140.0970.3223-0.07290.2220.0868-0.04830.3386-0.10260.287236.922-35.830937.3475
183.9158-0.72870.95781.937-0.93023.2586-0.2895-1.1603-1.25390.33790.34210.49920.7336-0.58660.00550.44440.06480.03170.80480.30470.798218.4985-50.919644.5838
193.36751.0361-0.72453.0325-1.03773.1184-0.02410.31460.1039-0.36010.25220.5904-0.2243-0.5079-0.20510.42880.0453-0.17550.41680.09570.445612.96539.5331151.7946
203.1575-0.8679-0.69592.39250.79272.0137-0.21050.4848-0.4342-0.59070.05210.05040.3080.0460.18370.4412-0.06830.00330.3875-0.11520.269440.8642-4.5405153.0169
212.59480.5843-0.35222.42480.22323.4417-0.20140.6331-0.2582-0.6508-0.023-0.54730.29190.69620.1650.6420.04560.24090.7066-0.09990.719364.8562-1.2166146.1063
223.91540.6079-0.44373.16-0.1571.78160.0758-0.2802-0.1203-0.2663-0.18750.89290.1266-0.71070.13150.5251-0.1055-0.10140.7615-0.19970.5096-16.113877.4876151.4233
232.2549-1.8897-1.31592.68261.39762.26150.0776-0.4202-0.59440.105-0.14930.09930.5977-0.00690.05820.5737-0.1158-0.19550.51190.20260.481110.224259.8005152.429
242.7148-0.48290.30013.0584-0.1692.54040.0518-0.1982-0.541-0.5865-0.0504-0.1960.13880.6482-0.02890.5460.07550.00350.63890.09690.433234.131561.7724144.6632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 14:375 )A14 - 375
2X-RAY DIFFRACTION2( CHAIN A AND RESID 376:585 )A376 - 585
3X-RAY DIFFRACTION3( CHAIN A AND RESID 586:817 )A586 - 817
4X-RAY DIFFRACTION4( CHAIN B AND RESID 13:375 )B13 - 375
5X-RAY DIFFRACTION5( CHAIN B AND RESID 376:585 )B376 - 585
6X-RAY DIFFRACTION6( CHAIN B AND RESID 586:817 )B586 - 817
7X-RAY DIFFRACTION7( CHAIN C AND RESID 14:375 )C14 - 375
8X-RAY DIFFRACTION8( CHAIN C AND RESID 376:585 )C376 - 585
9X-RAY DIFFRACTION9( CHAIN C AND RESID 586:817 )C586 - 817
10X-RAY DIFFRACTION10( CHAIN D AND RESID 12:375 )D12 - 375
11X-RAY DIFFRACTION11( CHAIN D AND RESID 376:585 )D376 - 585
12X-RAY DIFFRACTION12( CHAIN D AND RESID 586:817 )D586 - 817
13X-RAY DIFFRACTION13( CHAIN E AND RESID 14:375 )E14 - 375
14X-RAY DIFFRACTION14( CHAIN E AND RESID 376:585 )E376 - 585
15X-RAY DIFFRACTION15( CHAIN E AND RESID 586:817 )E586 - 817
16X-RAY DIFFRACTION16( CHAIN F AND RESID 15:375 )F15 - 375
17X-RAY DIFFRACTION17( CHAIN F AND RESID 376:585 )F376 - 585
18X-RAY DIFFRACTION18( CHAIN F AND RESID 586:817 )F586 - 817
19X-RAY DIFFRACTION19( CHAIN G AND RESID 14:375 )G14 - 375
20X-RAY DIFFRACTION20( CHAIN G AND RESID 376:585 )G376 - 585
21X-RAY DIFFRACTION21( CHAIN G AND RESID 586:817 )G586 - 817
22X-RAY DIFFRACTION22( CHAIN H AND RESID 14:375 )H14 - 375
23X-RAY DIFFRACTION23( CHAIN H AND RESID 376:585 )H376 - 585
24X-RAY DIFFRACTION24( CHAIN H AND RESID 586:817 )H586 - 817

+
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