[English] 日本語
Yorodumi
- PDB-6i4y: X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i4y
TitleX-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex
Components
  • Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
  • PRELI domain containing protein 3B
KeywordsLIPID TRANSPORT / Mitochondrial lipid transport / Complex / Phospholipid transporter / Apoptosis / Phosphatidylserine / PS transport
Function / homology
Function and homology information


regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding / maltose transport / maltodextrin transmembrane transport / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / carbohydrate transport / carbohydrate transmembrane transporter activity / DNA damage response, signal transduction by p53 class mediator / Mitochondrial protein degradation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / cellular response to UV / p53 binding / outer membrane-bounded periplasmic space / periplasmic space / apoptotic process / DNA damage response / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
PRELI/MSF1 domain / Slowmo/Ups family / PRELI-like family / PRELI/MSF1 domain profile. / Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...PRELI/MSF1 domain / Slowmo/Ups family / PRELI-like family / PRELI/MSF1 domain profile. / Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / TP53-regulated inhibitor of apoptosis 1 / Maltose/maltodextrin-binding periplasmic protein / PRELI domain containing protein 3B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMiliara, X. / Berry, J.-L. / Morgan, R.M.L. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M019403/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins.
Authors: Miliara, X. / Tatsuta, T. / Berry, J.L. / Rouse, S.L. / Solak, K. / Chorev, D.S. / Wu, D. / Robinson, C.V. / Matthews, S. / Langer, T.
History
DepositionNov 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4324
Polymers72,0672
Non-polymers3652
Water27015
1
A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules

A: Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1
B: PRELI domain containing protein 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8648
Polymers144,1334
Non-polymers7314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area10830 Å2
ΔGint-92 kcal/mol
Surface area49200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.020, 133.000, 146.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1 / Protein 15E1.1 / WF-1 / p53-inducible cell-survival factor / p53CSV


Mass: 48939.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, NCTC8450_00456, NCTC9775_03059, TRIAP1, 15E1.1, HSPC132
Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle
References: UniProt: A0A376KDN7, UniProt: O43715, UniProt: P0AEX9*PLUS
#2: Protein PRELI domain containing protein 3B / Protein slowmo homolog 2


Mass: 23127.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID3B, C20orf45, SLMO2, CGI-107 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B1
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.39 Å3/Da / Density % sol: 63.71 % / Description: multi plate ellipsoid shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate (60% v/v) pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.91→76.23 Å / Num. obs: 20182 / % possible obs: 99.6 % / Redundancy: 7.3 % / Net I/σ(I): 15.8
Reflection shellResolution: 2.91→3.014 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XZV

4xzv


Resolution: 2.91→76.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.368 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R: 1.404 / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29635 972 4.8 %RANDOM
Rwork0.20983 ---
obs0.21394 19209 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--8.88 Å20 Å2
3----8.21 Å2
Refinement stepCycle: 1 / Resolution: 2.91→76.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 24 15 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194632
X-RAY DIFFRACTIONr_bond_other_d0.0030.024055
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9496341
X-RAY DIFFRACTIONr_angle_other_deg1.09639399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26825.469192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70415660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
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_it5.5188.9532416
X-RAY DIFFRACTIONr_mcbond_other5.5038.9522415
X-RAY DIFFRACTIONr_mcangle_it8.56313.4223016
X-RAY DIFFRACTIONr_mcangle_other8.56413.4243017
X-RAY DIFFRACTIONr_scbond_it5.049.0052216
X-RAY DIFFRACTIONr_scbond_other5.0399.0052216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.03213.4153326
X-RAY DIFFRACTIONr_long_range_B_refined13.01513.41519175
X-RAY DIFFRACTIONr_long_range_B_other13.00713.41519160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.91→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 82 -
Rwork0.383 1374 -
obs--99.18 %

+
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