[English] 日本語
Yorodumi
- PDB-3kxc: Mutant transport protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kxc
TitleMutant transport protein
Components
  • Trafficking protein particle complex subunit 3
  • Trafficking protein particle complex subunit 6B
KeywordsTRANSPORT PROTEIN / heterodimer / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Lipoprotein / Palmitate / Transport
Function / homology
Function and homology information


vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / intra-Golgi vesicle-mediated transport / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / cis-Golgi network membrane ...vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / intra-Golgi vesicle-mediated transport / RAB GEFs exchange GTP for GDP on RABs / cis-Golgi network / cis-Golgi network membrane / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / trans-Golgi network / nervous system development / Golgi membrane / Golgi apparatus / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 3 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Trafficking protein particle complex subunit 3 / Trafficking protein particle complex subunit 6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKummel, D. / Heinemann, U.
CitationJournal: Cell.Mol.Life Sci. / Year: 2010
Title: Characterization of the self-palmitoylation activity of the transport protein particle component Bet3
Authors: Kummel, D. / Walter, J. / Heck, M. / Heinemann, U. / Veit, M.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Trafficking protein particle complex subunit 3
C: Trafficking protein particle complex subunit 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1463
Polymers39,8902
Non-polymers2561
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-21 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.172, 69.265, 121.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Trafficking protein particle complex subunit 3 / Bet3 / BET3 homolog


Mass: 21882.717 Da / Num. of mol.: 1 / Mutation: C68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43617
#2: Protein Trafficking protein particle complex subunit 6B / TPC6B


Mass: 18006.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86SZ2
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% PEG 3350, 0.2M Li2SO4, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97852 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2007
RadiationMonochromator: single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28200 / Num. obs: 26752 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.05 % / Rsym value: 0.063 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.15 % / Mean I/σ(I) obs: 3 / Num. unique all: 3311 / Rsym value: 0.501 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFH

2cfh


Resolution: 2→28.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.431 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23238 1403 5 %RANDOM
Rwork0.19622 ---
all0.19799 26643 --
obs0.19799 26643 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.625 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---0.2 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 18 99 2431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9713203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76124.906106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7891512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21065
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21659
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65321519
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54132375
X-RAY DIFFRACTIONr_scbond_it4.2424947
X-RAY DIFFRACTIONr_scangle_it5.786825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 102 -
Rwork0.264 1933 -
obs--100 %
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)
19.59247.1406-6.8426.8167-3.72737.6956-0.52131.03460.8012-0.80430.68161.0185-0.0938-0.6661-0.1602-0.0925-0.0123-0.0157-0.09310.0788-0.025-18.30562.27118.3248
23.7926-0.2954-0.824.39-0.73244.5654-0.0411-0.44490.01590.2924-0.0557-0.70280.18860.76780.0967-0.14490.06170.0185-0.02050.0329-0.0109-2.76562.675121.0386
32.15820.1162-1.0613.738-1.23127.0173-0.3550.7189-0.3311-0.90130.22340.23361.1562-0.6090.13160.2208-0.13610.05310.0587-0.07450.0092-12.3606-4.7028-2.1794
40.2088-0.8053-0.34513.1131.14345.62020.11250.20570.0937-0.2894-0.0160.3401-0.0432-0.436-0.0965-0.0763-0.01110.01530.0136-0.0014-0.0513-12.98557.7636-0.1015
53.47-2.01030.79685.15292.30986.0794-0.2373-0.44530.05540.16480.1633-0.2742-0.48750.1830.0739-0.14020.00950.0184-0.1002-0.0052-0.0667-7.694513.323819.9307
61.8868-0.8099-2.08977.81080.52814.1556-0.03590.0831-0.1641-0.804-0.0686-0.24180.38560.2120.10450.00050.0440.0848-0.0777-0.01-0.084-4.83711.42143.6595
72.0393-2.2475-3.20742.4773.53495.04460.06720.28480.1627-0.49270.0356-0.1788-0.8102-0.0005-0.1028-0.00420.01230.0458-0.12730.0092-0.0881-9.441217.39579.3739
810.9151-10.8081-7.245719.75810.207910.4266-0.1479-0.1111-0.1265-0.3240.1907-1.00750.69330.8665-0.04280.09240.07050.16130.06380.0143-0.0247-0.29692.1463-2.8181
98.33150.60161.6856.82421.407824.1488-0.35050.5307-0.18610.21870.18120.90880.3652-1.4120.16930.0485-0.14210.1160.02350.0231-0.0343-19.1962-5.335513.1782
1018.2419-0.8589-1.077112.584-17.231830.85810.2247-0.3873-0.3587-0.2201-0.8293-0.73891.1561.31970.60460.05830.06150.1187-0.10110.0510.0117-10.4237-8.581319.2975
119.2393-5.25286.39685.2816-3.73414.50780.36330.15790.0994-0.1016-0.3659-0.77660.56470.83290.0026-0.04440.0669-0.02210.04190.08230.0889-7.9853-7.300831.6408
1218.7034-0.8673-1.691313.17141.417420.31350.1476-0.42211.0852-0.316-0.16220.6638-0.975-1.29070.0146-0.07770.0620.0182-0.16370.0235-0.0152-24.98694.391627.292
139.28330.8051-6.105615.6851-0.472329.1633-0.2142-0.07810.72660.63460.14281.6676-1.4339-2.09030.0714-0.06540.09040.01880.09570.02770.1334-35.6076-3.920234.9302
143.55361.4061-3.90093.1632-1.81568.1898-0.08290.39890.1602-0.41090.18440.24210.3241-0.7934-0.1015-0.1033-0.0593-0.0528-0.07960.0364-0.0965-31.1134-11.137130.0443
159.98381.7725-5.35085.91741.56311.0448-0.32020.8715-0.3746-0.97580.181-0.30530.6124-0.60950.13920.1656-0.0550.0318-0.1074-0.0083-0.1206-24.7593-16.131224.0465
168.76671.4689-4.34884.65862.691614.9572-0.41450.1844-0.68330.0212-0.0277-0.88530.94631.02880.4422-0.06310.05690.0769-0.13250.0685-0.039-16.1726-10.98627.0419
174.6161-4.1323-0.598911.4743-2.350310.0811-0.1912-0.24840.56080.5130.2955-0.283-0.6694-0.0844-0.1043-0.1227-0.01340.0067-0.18020.0176-0.1101-24.5583-1.767136.4392
186.0344-1.31533.765810.49114.63214.41110.3350.089-0.9632-0.1077-0.0256-0.5821.70630.1199-0.30940.1274-0.03640.0526-0.17050.02260.0065-21.906-18.464130.1595
199.1002-3.04295.068728.711117.162530.3422-0.4044-0.73130.17850.88050.2322-0.6689-0.7463-0.00840.1722-0.107-0.0707-0.0418-0.06630.0158-0.1632-24.7269-5.796344.3286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 23
2X-RAY DIFFRACTION2A24 - 48
3X-RAY DIFFRACTION3A49 - 77
4X-RAY DIFFRACTION4A78 - 112
5X-RAY DIFFRACTION5A113 - 129
6X-RAY DIFFRACTION6A130 - 153
7X-RAY DIFFRACTION7A154 - 162
8X-RAY DIFFRACTION8A163 - 171
9X-RAY DIFFRACTION9C2 - 9
10X-RAY DIFFRACTION10C10 - 17
11X-RAY DIFFRACTION11C24 - 41
12X-RAY DIFFRACTION12C42 - 53
13X-RAY DIFFRACTION13C58 - 68
14X-RAY DIFFRACTION14C69 - 92
15X-RAY DIFFRACTION15C93 - 103
16X-RAY DIFFRACTION16C115 - 125
17X-RAY DIFFRACTION17C126 - 138
18X-RAY DIFFRACTION18C139 - 152
19X-RAY DIFFRACTION19C153 - 158

+
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