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- PDB-6y7f: Crystal structure of human ELOVL fatty acid elongase 7 (ELOVL7) -

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Basic information

Entry
Database: PDB / ID: 6y7f
TitleCrystal structure of human ELOVL fatty acid elongase 7 (ELOVL7)
ComponentsElongation of very long chain fatty acids protein 7
KeywordsTRANSFERASE / Fatty acid biosynthesis / Lipid biosynthesis / membrane protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


very-long-chain 3-oxoacyl-CoA synthase / fatty acid elongase activity / fatty acid elongation, monounsaturated fatty acid / fatty acid elongation, polyunsaturated fatty acid / long-chain fatty-acyl-CoA biosynthetic process / Synthesis of very long-chain fatty acyl-CoAs / very long-chain fatty acid biosynthetic process / unsaturated fatty acid biosynthetic process / fatty acid elongation, saturated fatty acid / sphingolipid biosynthetic process ...very-long-chain 3-oxoacyl-CoA synthase / fatty acid elongase activity / fatty acid elongation, monounsaturated fatty acid / fatty acid elongation, polyunsaturated fatty acid / long-chain fatty-acyl-CoA biosynthetic process / Synthesis of very long-chain fatty acyl-CoAs / very long-chain fatty acid biosynthetic process / unsaturated fatty acid biosynthetic process / fatty acid elongation, saturated fatty acid / sphingolipid biosynthetic process / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
ELO family / ELO family, conserved site / Elongation of very long chain fatty acids protein 7 / GNS1/SUR4 family / ELO family signature.
Similarity search - Domain/homology
Octyl Glucose Neopentyl Glycol / Chem-OFN / Very long chain fatty acid elongase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.052 Å
AuthorsNie, L. / Pike, A.C.W. / Bushell, S.R. / Chu, A. / Cole, V. / Speedman, D. / Rodstrom, K.E.J. / Kupinska, K. / Shrestha, L. / Mukhopadhyay, S.M.M. ...Nie, L. / Pike, A.C.W. / Bushell, S.R. / Chu, A. / Cole, V. / Speedman, D. / Rodstrom, K.E.J. / Kupinska, K. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Love, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Commission115766 United Kingdom
Wellcome Trust106169/Z/14/Z United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human ELOVL fatty acid elongase 7 (ELOVL7)
Authors: Nie, L. / Pike, A.C.W. / Bushell, S.R. / Chu, A. / Cole, V. / Speedman, D. / Kupinska, K. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Love, J. / Edwards, A.M. / Arrowsmith, ...Authors: Nie, L. / Pike, A.C.W. / Bushell, S.R. / Chu, A. / Cole, V. / Speedman, D. / Kupinska, K. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Love, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation of very long chain fatty acids protein 7
B: Elongation of very long chain fatty acids protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,01410
Polymers68,5162
Non-polymers4,4988
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS analysis supports dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-44 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.229, 72.459, 112.043
Angle α, β, γ (deg.)90, 100.03, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elongation of very long chain fatty acids protein 7 / 3-keto acyl-CoA synthase ELOVL7 / ELOVL fatty acid elongase 7 / ELOVL FA elongase 7 / Very long ...3-keto acyl-CoA synthase ELOVL7 / ELOVL fatty acid elongase 7 / ELOVL FA elongase 7 / Very long chain 3-ketoacyl-CoA synthase 7 / Very long chain 3-oxoacyl-CoA synthase 7


Mass: 34258.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOVL7 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A1L3X0, very-long-chain 3-oxoacyl-CoA synthase
#2: Chemical ChemComp-OFN / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneicosanethioate


Mass: 1076.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H72N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-37X / Octyl Glucose Neopentyl Glycol


Mass: 568.695 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H52O12
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30-36% PEG400 -- 0.1M acetate pH 4.5 -- 0.23M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.052→62.262 Å / Num. obs: 36724 / % possible obs: 58.7 % / Redundancy: 6.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.062 / Rrim(I) all: 0.119 / Net I/σ(I): 8.3
Reflection shellResolution: 2.052→2.182 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1837 / CC1/2: 0.813 / Rpim(I) all: 0.449 / Rrim(I) all: 0.839 / % possible all: 17.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALS2.0.3data reduction
STARANISO2.3.25data scaling
AutoSol1.17.1-3660phasing
RESOLVE1.17.1-3660phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.052→28.68 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.876 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.251 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.197
Details: Structure refined against STARANISO anisotropically truncated data. LSSR restraints were used and a single TLS group was refined for each chain. Heterogen dictionaries were generated using ...Details: Structure refined against STARANISO anisotropically truncated data. LSSR restraints were used and a single TLS group was refined for each chain. Heterogen dictionaries were generated using GRADE. ACCOMPANYING SF CIF CONTAINS STARANISO DATA USED FOR REFINEMENT ALONG WITH SCALED MERGED DATA WITHOUT TRUNCATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1765 5 %RANDOM
Rwork0.2104 ---
obs0.2112 36690 58.7 %-
Displacement parametersBiso mean: 43.99 Å2
Baniso -1Baniso -2Baniso -3
1-18.3797 Å20 Å2-2.8687 Å2
2---10.8681 Å20 Å2
3----7.5115 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.052→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 293 112 4650
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084733HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.876461HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2117SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes743HARMONIC5
X-RAY DIFFRACTIONt_it4733HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion597SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3786SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 2.052→2.1 Å
RfactorNum. reflection% reflection
Rfree0.1817 29 -
Rwork0.1967 --
obs--15.88 %
Refinement TLS params.

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)
11.1760.10330.27592.7466-0.57223.54730.06050.06780.04960.0678-0.03530.35280.04960.3528-0.0252-0.0551-0.0232-0.0421-0.3474-0.0327-0.308218.453436.417116.2398
21.43330.03580.43323.8033-0.69253.1779-0.13110.7265-0.08450.72650.0203-0.0766-0.0845-0.07660.11090.11170.0433-0.0494-0.3438-0.0676-0.320711.49866.469734.366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|16 - 301}
2X-RAY DIFFRACTION2{B|14 - 301}

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