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- PDB-5kyx: crystal structure of Sec23 and TANGO1 peptide1 complex -

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Basic information

Entry
Database: PDB / ID: 5kyx
Titlecrystal structure of Sec23 and TANGO1 peptide1 complex
Components
  • Protein transport protein Sec23AProtein targeting
  • Protein transport protein Sec24DProtein targeting
KeywordsPROTEIN TRANSPORT / COPII coat / collagen secretion / cargo adapter / vesicle
Function / homology
Function and homology information


COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / GTPase activator activity / SNARE binding ...COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / in utero embryonic development / 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 / 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 / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.516 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0284
Polymers172,8972
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area62360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.956, 141.871, 152.434
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.22 Å3/Da / Density % sol: 61.79 %
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: 3.4→50 Å / Num. obs: 25117 / % possible obs: 99.7 % / Redundancy: 2.9 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.516→48.772 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2002 7.97 %
Rwork0.1947 --
obs0.1996 25117 88.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.516→48.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11704 0 2 0 11706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311984
X-RAY DIFFRACTIONf_angle_d0.73716229
X-RAY DIFFRACTIONf_dihedral_angle_d14.4334489
X-RAY DIFFRACTIONf_chiral_restr0.0281806
X-RAY DIFFRACTIONf_plane_restr0.0042109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5162-3.60420.2657960.2551143X-RAY DIFFRACTION63
3.6042-3.70160.31451260.25641338X-RAY DIFFRACTION73
3.7016-3.81050.31941080.2491366X-RAY DIFFRACTION74
3.8105-3.93340.30541320.24681513X-RAY DIFFRACTION82
3.9334-4.07390.30621390.22221606X-RAY DIFFRACTION86
4.0739-4.23690.30111360.20721653X-RAY DIFFRACTION90
4.2369-4.42960.2241600.18341695X-RAY DIFFRACTION92
4.4296-4.6630.24981350.17541757X-RAY DIFFRACTION94
4.663-4.95490.22081500.17351759X-RAY DIFFRACTION95
4.9549-5.3370.22391640.18421787X-RAY DIFFRACTION96
5.337-5.87330.25311580.20161868X-RAY DIFFRACTION99
5.8733-6.72130.24871550.21241851X-RAY DIFFRACTION98
6.7213-8.46090.27081680.19251830X-RAY DIFFRACTION96
8.4609-48.77660.23361750.16121949X-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)
1-0.0568-0.21790.04330.3571-0.1889-0.01720.32970.1367-0.9041-0.00710.0637-0.7175-0.0188-0.07470.00260.596-0.0301-0.12110.6366-0.06170.7518.7719-96.3493-9.8694
20.0775-0.02260.1409-0.0095-0.03560.14680.10680.3552-0.25370.117-0.15840.1243-0.04630.092200.7619-0.0383-0.23920.73430.05350.912221.4123-88.46382.9601
30.43240.4263-0.20320.93650.86540.85150.015-0.04650.10110.06220.0170.0142-0.15430.023300.6012-0.04910.04690.58870.01030.62535.8126-67.2032-9.6889
40.33370.15050.18470.00330.58880.3373-0.03520.166-0.2465-0.07740.0847-0.40280.06510.129800.68380.00920.01360.6371-0.09650.58088.4063-92.9533-27.57
50.02040.01070.12980.1201-0.02980.2688-0.38380.2011-0.08330.05040.05690.4845-0.0325-0.06040.00020.5703-0.03270.04480.6757-0.04731.1554-18.0325-93.2475-20.0352
60.2213-0.180.36170.2553-0.56880.40090.22530.22880.21420.05660.21650.3710.1478-0.53370.01040.6498-0.0122-0.15420.7645-0.14290.6964-12.4874-90.3078-24.5251
7-0.0263-0.1858-0.01331.59790.28880.58620.0225-0.0601-0.0447-0.0514-0.10160.1409-0.0243-0.073700.47750.02140.03660.58-0.03980.6351-1.2767-11.5559-8.2182
80.12080.50910.20171.10620.49490.07790.1803-0.1584-0.05340.308-0.2248-0.6736-0.03340.2621-00.7908-0.0708-0.03490.7599-0.01210.89714.69955.20446.0023
90.0059-0.21540.02060.37240.49490.3338-0.51920.16350.3475-0.3319-0.09070.1436-0.1512-0.0741-0.00010.81260.0084-0.18710.83430.07330.978614.74682.032811.6934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 491 )
4X-RAY DIFFRACTION4chain 'A' and (resid 492 through 607 )
5X-RAY DIFFRACTION5chain 'A' and (resid 608 through 678 )
6X-RAY DIFFRACTION6chain 'A' and (resid 679 through 762 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 802 )
8X-RAY DIFFRACTION8chain 'B' and (resid 803 through 952 )
9X-RAY DIFFRACTION9chain 'B' and (resid 953 through 1033 )

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