[English] 日本語
Yorodumi
- PDB-7ff6: The 0.83 angstrom X-ray structure of the human heart fatty acid-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ff6
TitleThe 0.83 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with cis-vaccenic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / complex / binding protein / cis-vaccenic acid
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
cis-vaccenic acid / Chem-GLP / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.83 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Nakano, R. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support Japan, Jamaica, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Science and TechnologyJPMJER1005 Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Other private09-003-005Jamaica
CitationJournal: To Be Published
Title: The 0.83 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with cis-vaccenic acid
Authors: Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
History
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9855
Polymers14,8791
Non-polymers1,1064
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-2 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.656, 69.730, 33.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 14879.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#2: Chemical ChemComp-4IF / cis-vaccenic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14NO8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Mes-NaOH (pH6.5), 45% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.83→50 Å / Num. obs: 116840 / % possible obs: 95.7 % / Redundancy: 9.2 % / Rpim(I) all: 0.03 / Net I/σ(I): 9.9
Reflection shellResolution: 0.83→0.84 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5602 / Rpim(I) all: 0.251

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVM

3wvm


Resolution: 0.83→28.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.321 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12966 5766 4.9 %RANDOM
Rwork0.1208 ---
obs0.12123 111032 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 0.83→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 71 212 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0131412
X-RAY DIFFRACTIONr_bond_other_d0.0170.0181395
X-RAY DIFFRACTIONr_angle_refined_deg2.571.7181910
X-RAY DIFFRACTIONr_angle_other_deg1.8181.723283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21824.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.937155
X-RAY DIFFRACTIONr_chiral_restr0.1080.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021580
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02271
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_it1.3810.731668
X-RAY DIFFRACTIONr_mcbond_other1.2710.727666
X-RAY DIFFRACTIONr_mcangle_it1.6331.108870
X-RAY DIFFRACTIONr_mcangle_other1.6331.109871
X-RAY DIFFRACTIONr_scbond_it2.6491.032744
X-RAY DIFFRACTIONr_scbond_other2.6491.031744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9271.4421041
X-RAY DIFFRACTIONr_long_range_B_refined3.9411.3011589
X-RAY DIFFRACTIONr_long_range_B_other3.48110.5081529
X-RAY DIFFRACTIONr_rigid_bond_restr9.90632806
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.83→0.851 Å
RfactorNum. reflection% reflection
Rfree0.274 375 -
Rwork0.259 7727 -
obs--90.81 %

+
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