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- PDB-5kyw: crystal structure of Sec23 and TANGO1 peptide3 complex -

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Basic information

Entry
Database: PDB / ID: 5kyw
Titlecrystal structure of Sec23 and TANGO1 peptide3 complex
Components
  • Protein transport protein Sec23AProtein targeting
  • Protein transport protein Sec24DProtein targeting
  • TANGO1 peptide3
KeywordsPROTEIN TRANSPORT / COPII coat / collagen secretion / cargo adapter / vesicle
Function / homology
Function and homology information


vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / COPII-coated vesicle cargo loading / cellular response to oxidised low-density lipoprotein particle stimulus / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion ...vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / COPII-coated vesicle cargo loading / cellular response to oxidised low-density lipoprotein particle stimulus / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion / endoplasmic reticulum organization / cell migration involved in sprouting angiogenesis / cargo receptor activity / COPII-mediated vesicle transport / positive regulation of leukocyte migration / lipoprotein transport / exocytosis / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / GTPase activator activity / SNARE binding / negative regulation of cell migration / protein localization to plasma membrane / Post-translational protein phosphorylation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / wound healing / ER to Golgi transport vesicle membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein transport / in utero embryonic development / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / membrane / cytosol
Similarity search - Function
Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich ...Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / Variant SH3 domain / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein transport protein Sec24D / Protein transport protein Sec23A / Transport and Golgi organization protein 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: TANGO1/cTAGE5 receptor as a polyvalent template for assembly of large COPII coats.
Authors: Ma, W. / Goldberg, J.
History
DepositionJul 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24D
C: TANGO1 peptide3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9405
Polymers173,8093
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area61490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.625, 141.346, 151.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein transport protein Sec23A / Protein targeting / SEC23-related protein A


Mass: 86249.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15436
#2: Protein Protein transport protein Sec24D / Protein targeting / SEC24-related protein D


Mass: 86647.852 Da / Num. of mol.: 1 / Fragment: unp residues 266-1032
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D, KIAA0755
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O94855
#3: Protein/peptide TANGO1 peptide3


Mass: 912.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JRA6*PLUS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTANGO1 peptide3 LPPPFGPGM is derived from human TANGO1 protein (1800-1808)

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 5.5 % (w/v) PEG 4000, 100 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→82.512 Å / Num. obs: 36535 / % possible obs: 99.9 % / Redundancy: 3.2 % / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.2→82.512 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1827 5 %
Rwork0.21 --
obs0.2124 36535 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→82.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11697 0 2 0 11699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311959
X-RAY DIFFRACTIONf_angle_d0.58816200
X-RAY DIFFRACTIONf_dihedral_angle_d11.6287266
X-RAY DIFFRACTIONf_chiral_restr0.0421805
X-RAY DIFFRACTIONf_plane_restr0.0042104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.28660.4091560.36922598X-RAY DIFFRACTION99
3.2866-3.38330.37251430.32722636X-RAY DIFFRACTION99
3.3833-3.49250.32781250.3052634X-RAY DIFFRACTION100
3.4925-3.61730.39731280.28332661X-RAY DIFFRACTION100
3.6173-3.76220.27881330.26072642X-RAY DIFFRACTION100
3.7622-3.93340.29131250.22692659X-RAY DIFFRACTION100
3.9334-4.14080.261390.20632663X-RAY DIFFRACTION100
4.1408-4.40020.23481610.17652642X-RAY DIFFRACTION100
4.4002-4.73990.19791290.16622678X-RAY DIFFRACTION100
4.7399-5.21680.21321440.17052678X-RAY DIFFRACTION100
5.2168-5.97150.24161460.19462696X-RAY DIFFRACTION100
5.9715-7.52270.28581590.2162715X-RAY DIFFRACTION99
7.5227-82.53950.1931390.16872806X-RAY DIFFRACTION97
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)
15.4779-0.38373.63924.686-0.40824.8560.3666-0.2839-1.1562-0.38350.15470.57270.4253-0.4569-0.53690.52230.0312-0.05930.62040.06120.8983-22.7599-96.42276.4774
24.77753.56141.29068.12210.47971.3631-0.08690.5274-0.5183-0.83440.27280.36060.0596-0.2742-0.24920.61770.1297-0.02030.792-0.0480.7728-14.2095-82.8336-3.2379
32.40350.19210.78765.13771.94413.81780.01650.47680.3342-0.4355-0.0192-0.1668-0.24760.089-0.03410.81450.02480.11120.63750.14640.8706-2.2808-56.3951-0.6595
42.9940.79430.46624.2003-0.0531.69940.0022-0.14470.16480.21530.03380.2645-0.2151-0.1048-0.03340.64560.1184-0.00990.57810.04740.5898-6.4947-68.866114.3834
53.75180.54161.33423.2862-1.0985.52780.0833-0.9802-0.80720.29730.18180.39640.1639-0.7983-0.2310.47650.07670.22880.7240.18490.7739-15.7483-92.011420.454
64.1028-0.30440.41064.10520.01442.22240.0155-0.5656-0.69540.35130.1416-0.5708-0.00290.1227-0.07130.60520.0275-0.07060.71530.14440.73389.7135-91.543124.7524
71.57580.33950.25954.9722-0.01352.0964-0.0029-0.1713-0.06140.3532-0.08-0.092-0.09690.23650.05150.4633-0.01930.0360.60930.1060.53720.541-11.36828.5485
82.2888-0.5858-0.1714.751-0.30666.00370.09050.17690.1354-0.6719-0.12540.5945-0.4456-0.2639-0.04320.52050.0727-0.09160.59480.01170.9112-15.19525.1569-6.2914
93.59170.60461.19274.773-1.71767.1031-0.30010.09950.5182-0.0544-0.12430.0167-0.6826-0.30890.2890.7110.0788-0.20970.67630.03471.049-14.97872.168-11.4795
103.47383.20713.64292.9733.36523.8219-0.23220.05510.2813-0.33650.00910.3521-0.3648-0.07640.21651.7340.6778-0.30782.01130.0452.33734.9696-100.678120.2379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 456 )
5X-RAY DIFFRACTION5chain 'A' and (resid 457 through 557 )
6X-RAY DIFFRACTION6chain 'A' and (resid 558 through 762 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 802 )
8X-RAY DIFFRACTION8chain 'B' and (resid 803 through 955 )
9X-RAY DIFFRACTION9chain 'B' and (resid 956 through 1032 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1801 through 1803 )

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