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- PDB-4ymk: Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 -

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Basic information

Entry
Database: PDB / ID: 4ymk
TitleCrystal Structure of Stearoyl-Coenzyme A Desaturase 1
ComponentsAcyl-CoA desaturase 1
KeywordsOXIDOREDUCTASE / dimetal center
Function / homology
Function and homology information


stearoyl-CoA 9-desaturase / stearoyl-CoA 9-desaturase activity / palmitoyl-CoA 9-desaturase activity / Fatty acyl-CoA biosynthesis / tarsal gland development / unsaturated fatty acid biosynthetic process / sebaceous gland development / monounsaturated fatty acid biosynthetic process / sterol homeostasis / response to fatty acid ...stearoyl-CoA 9-desaturase / stearoyl-CoA 9-desaturase activity / palmitoyl-CoA 9-desaturase activity / Fatty acyl-CoA biosynthesis / tarsal gland development / unsaturated fatty acid biosynthetic process / sebaceous gland development / monounsaturated fatty acid biosynthetic process / sterol homeostasis / response to fatty acid / triglyceride metabolic process / lipid biosynthetic process / lipid homeostasis / white fat cell differentiation / brown fat cell differentiation / cholesterol homeostasis / response to bacterium / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / oxidoreductase activity / defense response to Gram-positive bacterium / iron ion binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / membrane / metal ion binding
Similarity search - Function
Fatty acid desaturase type 1, conserved site / Acyl-CoA desaturase / Fatty acid desaturases family 1 signature. / Fatty acid desaturase domain / Fatty acid desaturase
Similarity search - Domain/homology
Chem-MPG / STEAROYL-COENZYME A / Acyl-CoA desaturase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.605 Å
AuthorsBai, Y. / McCoy, J.G. / Rajashankar, K.R. / Zhou, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098878 United States
CitationJournal: Nature / Year: 2015
Title: X-ray structure of a mammalian stearoyl-CoA desaturase.
Authors: Bai, Y. / McCoy, J.G. / Levin, E.J. / Sobrado, P. / Rajashankar, K.R. / Fox, B.G. / Zhou, M.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Structure summary
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jun 8, 2016Group: Atomic model
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA desaturase 1
D: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,18410
Polymers79,1412
Non-polymers3,0438
Water1,54986
1
A: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0925
Polymers39,5711
Non-polymers1,5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl-CoA desaturase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0925
Polymers39,5711
Non-polymers1,5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.061, 113.766, 141.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acyl-CoA desaturase 1 / Delta(9)-desaturase 1 / Delta-9 desaturase 1 / Fatty acid desaturase 1 / Stearoyl-CoA desaturase 1


Mass: 39570.629 Da / Num. of mol.: 2 / Fragment: UNP residues 24-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scd1 / Plasmid: pFastBacDUAL / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13516, stearoyl-CoA 9-desaturase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ST9 / STEAROYL-COENZYME A / Stearoyl-CoA


Mass: 1033.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H70N7O17P3S
#4: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.1370.2
24.1370.2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981lipidic cubic phase6.935% PEG400, 200 mM sodium chloride, 4% ethylene glycol, 100 mM MES, pH 6.9
2982lipidic cubic phase6.935% PEG400, 200 mM sodium chloride, 4% ethylene glycol, 100 mM MES, pH 6.9

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2932
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9795
SYNCHROTRONAPS 24-ID-C21.2541
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELNov 18, 2013
DECTRIS PILATUS 6M-F2PIXELMar 8, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.25411
ReflectionNumber: 248246 / Rmerge(I) obs: 0.185 / Χ2: 1.07 / D res high: 2.79 Å / Num. obs: 59494 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
2.792.87388011.545
2.872.94433011.425
2.943.03416211.122
3.033.12413210.872
3.123.23397310.725
3.233.34382610.566
3.343.46369110.457
3.463.61354010.395
3.613.77339710.319
3.773.95333610.259
3.954.16305310.203
4.164.42296010.168
4.424.72275710.142
4.725.1257410.111
5.15.59234810.113
5.596.25215410.109
6.257.21188210.086
7.218.83160010.064
8.8312.49123510.048
ReflectionResolution: 2.6→50 Å / Num. obs: 38065 / % possible obs: 98 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.5 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Χ2: 0.933 / Net I/av σ(I): 14.407 / Net I/σ(I): 6.9 / Num. measured all: 237283 / Scaling rejects: 83
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible allMean I/σ(I) obsNum. measured all
2.6-2.6450.5318130.8270.2480.5880.81394
2.64-2.695.60.51918240.8650.2290.5690.86196.8
2.69-2.7460.45418630.8980.1960.4960.8997
2.74-2.86.20.39418570.9230.1680.4290.89298.4
2.8-2.866.30.35718960.9260.1510.3880.96598.3
2.86-2.936.30.3218890.9470.1360.3490.95198.6
2.93-36.20.2718820.9520.1160.2941.00798.7
3-3.085.90.23218480.9580.1020.2541.03794.8
3.08-3.176.60.21718770.9740.090.2351.04798.9
3.17-3.286.60.18419020.9780.0760.21.07299.2
3.28-3.396.50.15919110.980.0660.1731.01899.2
3.39-3.536.40.14419220.9840.060.1561.00799.2
3.53-3.696.20.12219040.9860.0520.1330.94699
3.69-3.886.10.10718920.9870.0460.1170.94497.4
3.88-4.136.70.09519290.9930.0390.1020.89699.2
4.13-4.456.60.08619420.9920.0360.0930.86499.4
4.45-4.896.30.08219630.9940.0350.0890.86399.4
4.89-5.66.50.07519050.9960.0310.0810.88497.2
5.6-7.056.40.06820030.9960.0290.0740.86499.527.37903
7.05-506.20.0420430.9990.0180.0450.79996.51.332391

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
SHELXDEphasing
PHASERphasing
HKL-2000data scaling
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.605→47.411 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1999 5.26 %Random selection
Rwork0.2027 36017 --
obs0.2044 38016 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.08 Å2 / Biso mean: 46.8574 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 2.605→47.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 188 86 5505
Biso mean--51.48 40.97 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025587
X-RAY DIFFRACTIONf_angle_d0.6337565
X-RAY DIFFRACTIONf_chiral_restr0.03779
X-RAY DIFFRACTIONf_plane_restr0.002928
X-RAY DIFFRACTIONf_dihedral_angle_d14.0872022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6054-2.67060.2651340.22122418255293
2.6706-2.74280.24071390.2162509264897
2.7428-2.82350.2791410.2092520266198
2.8235-2.91460.26321420.19972554269698
2.9146-3.01870.241410.20582550269199
3.0187-3.13960.27571390.20612512265196
3.1396-3.28240.2261430.21082583272699
3.2824-3.45540.24681440.20252581272599
3.4554-3.67190.24331450.20512617276299
3.6719-3.95520.22761420.20582549269198
3.9552-4.3530.22611450.210426262771100
4.353-4.98230.26641450.20222600274598
4.9823-6.27490.21811470.20172667281499
6.2749-47.41880.18351520.1812731288397
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)
12.20290.21010.13341.51570.72954.9202-0.03160.0765-0.1567-0.03050.0760.062-0.0392-0.3184-0.03620.27310.04990.00790.21850.08490.3217-27.3078-18.963915.0396
21.70180.02740.22470.78040.19062.4939-0.09690.03610.07770.04650.02-0.0397-0.0804-0.06580.07690.24750.0057-0.00860.29610.01330.2688-20.197-18.513410.0211
32.3639-1.75060.43981.9354-2.48498.3357-0.02270.8318-0.0201-0.23450.26540.1908-0.49240.388-0.30680.6407-0.11340.06330.558-0.09940.449113.636925.5101-0.7659
42.99090.8060.66831.49180.89082.14280.0843-0.4503-0.16320.2436-0.12910.06410.0774-0.03370.0370.3835-0.06690.01770.3888-0.00380.26831.895816.936821.5934
58.9659-2.55630.98024.15650.27852.2281-0.0593-0.0431-0.0012-0.36440.2409-0.0723-0.4180.3431-0.18760.4891-0.1679-0.00330.40780.01010.288511.667225.68617.4232
62.2016-0.03450.75133.0749-0.66555.7219-0.0169-0.87220.22030.5781-0.2638-0.1632-0.1031-0.18620.15960.5368-0.08250.06730.6814-0.10340.344-0.114622.665130.1883
72.17070.91472.24363.06092.13618.7452-0.00020.2179-0.1782-0.26280.208-0.28930.30820.0955-0.18640.3211-0.04660.01990.2950.01420.33126.81699.47266.9211
87.4725-1.8133-3.78853.29721.59467.9273-0.04920.6458-0.2494-0.555-0.10470.17190.2565-0.61210.24450.4189-0.1349-0.00860.2883-0.04280.3126-4.42229.22660.0404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 112 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 361 )A0
3X-RAY DIFFRACTION3chain 'D' and (resid 41 through 68 )D0
4X-RAY DIFFRACTION4chain 'D' and (resid 69 through 141 )D0
5X-RAY DIFFRACTION5chain 'D' and (resid 142 through 204 )D0
6X-RAY DIFFRACTION6chain 'D' and (resid 205 through 246 )D0
7X-RAY DIFFRACTION7chain 'D' and (resid 247 through 314 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 315 through 352 )D0

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