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- PDB-5kyn: Structure of Sec23 and TANGO1 complex -

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Basic information

Entry
Database: PDB / ID: 5kyn
TitleStructure of Sec23 and TANGO1 complex
Components
  • Melanoma inhibitory activity protein 3
  • Protein transport protein Sec23A
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 / positive regulation of leukocyte migration / COPII-mediated vesicle transport / cargo receptor activity / lipoprotein transport / endoplasmic reticulum exit site / exocytosis / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / GTPase activator activity / 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 / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / 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 / 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 / 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 / Variant SH3 domain / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A 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 Sec23A / Transport and Golgi organization protein 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 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 21, 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 Sec23A
C: Melanoma inhibitory activity protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4615
Polymers173,3303
Non-polymers1312
Water59433
1
A: Protein transport protein Sec23A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3152
Polymers86,2491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area31910 Å2
MethodPISA
2
B: Protein transport protein Sec23A
C: Melanoma inhibitory activity protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1463
Polymers87,0802
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-4 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.454, 65.880, 229.871
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 86249.492 Da / Num. of mol.: 2
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/peptide Melanoma inhibitory activity protein 3


Mass: 830.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JRA6*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FULL CRYSTALLIZED SEQUENCE CORRESPONDS TO THE FOLLOWING DOMAIN: ...THE FULL CRYSTALLIZED SEQUENCE CORRESPONDS TO THE FOLLOWING DOMAIN: PPPIRYGPPPQLCGPFGPRPLPPPFGPGMRPPLGLREFAPGVPPGRRDLPLHPRGFLPGHA. MOST OF THE PROTEIN WAS DISORDERED AND COULD NOT BE LOCATED FROM THE ELECTRON DENSITY. GENE NAME: MIA3, KIAA0268, TANGO, TANGO1, UNQ6077/PRO20088

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES PH 7.5, 6% (v/v ) isopropanol and 300 mM sodium citrate

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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: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 57059 / % possible obs: 99.8 % / Redundancy: 2.9 % / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EGD

3egd


Resolution: 2.552→47.94 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1997 3.5 %
Rwork0.2001 --
obs0.2018 57059 87.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.552→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11393 0 2 33 11428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211660
X-RAY DIFFRACTIONf_angle_d0.56315810
X-RAY DIFFRACTIONf_dihedral_angle_d12.3717022
X-RAY DIFFRACTIONf_chiral_restr0.0421749
X-RAY DIFFRACTIONf_plane_restr0.0042047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5523-2.61610.4637880.33722438X-RAY DIFFRACTION55
2.6161-2.68680.30311030.30942840X-RAY DIFFRACTION64
2.6868-2.76590.37211190.28483273X-RAY DIFFRACTION73
2.7659-2.85510.28971330.27073685X-RAY DIFFRACTION83
2.8551-2.95720.30861540.26124228X-RAY DIFFRACTION95
2.9572-3.07550.32131560.25894305X-RAY DIFFRACTION97
3.0755-3.21550.27781560.25274307X-RAY DIFFRACTION97
3.2155-3.3850.31540.23884262X-RAY DIFFRACTION95
3.385-3.5970.28241490.21764093X-RAY DIFFRACTION92
3.597-3.87460.23851580.20264371X-RAY DIFFRACTION98
3.8746-4.26430.23531570.17864319X-RAY DIFFRACTION97
4.2643-4.88080.18441520.15824196X-RAY DIFFRACTION93
4.8808-6.14730.22961610.18524418X-RAY DIFFRACTION97
6.1473-47.94830.22981570.17354327X-RAY DIFFRACTION93
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)
14.9521-0.40042.74952.039-0.24014.2398-0.1749-0.22840.02150.24370.1329-0.0741-0.2828-0.05960.04490.49450.0330.07270.2643-0.03290.285720.6212-50.1321107.6806
22.82880.7131.52653.5785-1.85345.5637-0.018-0.24410.04380.4992-0.0642-0.3884-0.19540.8727-0.04240.4833-0.0363-0.04780.4621-0.04750.415634.9237-45.186111.8393
31.82320.56240.33762.28360.1793.6954-0.07130.9180.366-0.43120.0561-0.5111-0.5231.00320.05791.0678-0.43040.27241.68330.1380.786341.6785-36.078368.7721
41.97540.10620.1481.4929-0.87664.3289-0.10420.79970.0039-0.3740.1034-0.1548-0.23410.6244-0.02020.5991-0.10250.10180.6821-0.0420.431925.2836-47.256980.6151
55.41620.85941.39271.7388-0.71893.1565-0.08040.1451-0.1318-0.16720.20390.18880.0102-0.0819-0.12030.44540.00920.07210.1822-0.01720.356812.2336-51.133895.8143
65.9431.25610.23212.6192-0.72495.5609-0.00990.30350.2632-0.18850.20680.5432-0.1467-0.5438-0.07190.5381-0.0092-0.02720.32180.04480.47031.2363-45.523185.3398
74.308-2.006-0.69445.67860.16522.1785-0.35130.1911.4263-0.30310.09140.2302-1.4451-0.67730.17481.2690.1118-0.2520.68710.09351.01943.6011-21.900284.1326
86.196-2.4617-0.4775.4699-5.13319.59890.4091.7943-0.01190.8465-0.8354-0.6422-2.16060.10960.49321.2343-0.2628-0.23671.10760.0660.7108-6.8095-45.401477.0978
97.15745.6492-5.99744.6907-5.16925.75920.3992-0.17021.0781-0.90730.19422.0189-0.1144-1.3221-0.84310.49810.0074-0.07710.78970.1230.9016-12.0655-49.309386.8618
104.6677-0.4139-0.91888.003-4.09452.3892-0.12460.0255-0.4415-1.05850.54280.0270.80580.39650.15560.6582-0.12990.08531.5409-0.08870.739615.2584-63.251611.7562
111.8315-0.8031-1.01013.9646-1.25745.23910.1292-0.0963-0.0187-0.2033-0.3881-0.443-0.3211.04260.03350.5251-0.0920.16981.41350.07960.65818.4829-60.263822.72
123.032-1.3101-0.91162.6016-1.26765.2229-0.2492-0.1033-0.7353-0.0317-0.3367-0.67371.1441.00580.47840.83520.31850.26221.99030.17441.024531.2326-76.419225.7491
132.203-1.4336-1.59654.36840.75478.79440.05080.6025-0.70160.2572-0.41630.64370.2994-0.74280.32230.6408-0.10010.21960.90880.0520.745-6.3284-71.574240.7542
148.1494-3.6893-3.86724.482.97672.8049-0.24170.0675-1.167-0.13040.37450.49250.8378-0.85390.3950.62930.03830.3221.1440.25960.7521-7.7395-73.957646.9442
152.8519-0.3212-1.23423.84890.42848.1436-0.6173-0.2133-1.5404-0.13240.34321.35350.5801-0.16370.45011.13230.07570.29491.46850.05921.0958-14.2603-72.806857.6206
165.692-0.5613-1.69734.35130.50152.167-0.4687-0.49-0.18721.55350.7017-0.4092-0.80490.35160.09891.28720.03880.12451.5630.13470.6799-3.01-65.262361.8748
171.4003-1.5538-0.21547.08880.4734.78920.5798-0.4756-0.86540.8817-0.36051.29141.131-0.6428-0.14241.2178-0.06130.43151.33840.05551.0888-11.0034-79.267250.6846
182.5845-0.2858-1.49413.3753-0.71683.25010.0471-0.1910.34370.58310.17130.363-0.7881-0.2307-0.23771.08220.07470.3361.43760.06140.7233-8.1522-53.792847.6843
192.8111.22461.71485.4132-0.79845.18510.42380.236-0.0535-0.531-0.33740.5617-0.1166-0.8661-0.07630.76460.07010.31641.45370.14660.684-12.6061-63.140933.486
207.65913.3271-2.9586.4065-1.56442.98610.1038-0.6254-0.2230.4208-0.214-0.3894-0.19911.11280.09420.641-0.05870.13491.48430.01680.52314.8017-61.33933.8709
216.80241.736-2.47643.3916-0.96493.0269-0.9155-0.5222-1.0485-0.43780.0116-0.68731.08510.92760.87830.62540.06890.22841.42990.0690.732417.6244-69.195829.2823
224.3284-1.236-1.81514.0712-0.16013.0504-0.16731.06320.5496-0.84690.1063-0.8225-1.05780.97350.11910.8481-0.39940.32341.81010.08161.002926.3655-49.562512.5076
235.2137-1.00271.22916.80561.38020.6244-0.34950.0460.72040.01170.4845-0.7396-0.75040.2218-0.1151.0024-0.21030.19841.05760.01490.688510.7845-41.414225.0985
245.1097-1.13581.96177.7285-0.57344.60850.15760.85471.5847-2.3315-0.2649-0.8548-0.75981.20410.17921.6588-0.32560.41711.53510.14981.075515.3724-36.20586.152
254.16133.61960.71666.1718-3.01664.36940.6182-0.13650.23130.8684-0.01090.5409-2.1532-0.0809-0.47451.24510.12640.3311.05630.28650.79560.1664-42.390121.7516
261.48080.31170.02841.3736-1.49651.7194-0.04560.8240.08070.470.31560.4729-1.0021-0.473-0.20690.77620.22870.31741.68030.22620.7933-7.7533-52.000916.7176
271.74091.3109-1.01881.1224-1.0231.1559-0.45390.2489-0.15310.39680.15381.51750.8938-1.73630.11180.8522-0.06670.69763.50030.85561.7231-29.6858-53.0325.5156
288.1431-1.34393.56033.8767-0.54419.54250.93060.86650.0435-0.27510.16880.98141.7411-0.517-0.70650.891-0.19870.11561.66440.30860.9968-20.5815-62.56198.3118
291.82891.8419-0.15823.7996-4.01967.2859-0.00080.5671-0.0070.35220.00950.4635-1.3428-1.3562-0.03361.02720.31720.33721.63330.09710.8237-15.3456-51.062220.1846
301.97540.6828-0.59294.5819-3.87193.27091.7175-4.8783.57963.0965-2.46611.5106-0.5048-3.04160.34281.3712-0.15930.26411.8748-0.37631.3239-1.7316-33.368817.4475
316.8964-1.49553.38442.89031.04252.897-2.49891.17591.4845-0.22871.0113-0.7901-1.6233-0.16860.88732.2214-0.34240.40071.39790.26920.99377.2579-31.730611.8804
326.5189-5.02933.04965.8834-1.5921.71580.2688-0.16110.1791-0.152-0.3643-0.2838-0.5436-1.8939-0.81031.0348-0.3217-0.14993.12981.26671.2673-28.4839-52.8768-3.083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 475 )
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 557 )
6X-RAY DIFFRACTION6chain 'A' and (resid 558 through 609 )
7X-RAY DIFFRACTION7chain 'A' and (resid 610 through 722 )
8X-RAY DIFFRACTION8chain 'A' and (resid 723 through 748 )
9X-RAY DIFFRACTION9chain 'A' and (resid 749 through 762 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 114 )
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 157 )
14X-RAY DIFFRACTION14chain 'B' and (resid 158 through 169 )
15X-RAY DIFFRACTION15chain 'B' and (resid 170 through 185 )
16X-RAY DIFFRACTION16chain 'B' and (resid 186 through 209 )
17X-RAY DIFFRACTION17chain 'B' and (resid 225 through 246 )
18X-RAY DIFFRACTION18chain 'B' and (resid 247 through 367 )
19X-RAY DIFFRACTION19chain 'B' and (resid 368 through 389 )
20X-RAY DIFFRACTION20chain 'B' and (resid 390 through 464 )
21X-RAY DIFFRACTION21chain 'B' and (resid 465 through 502 )
22X-RAY DIFFRACTION22chain 'B' and (resid 503 through 518 )
23X-RAY DIFFRACTION23chain 'B' and (resid 519 through 557 )
24X-RAY DIFFRACTION24chain 'B' and (resid 558 through 574 )
25X-RAY DIFFRACTION25chain 'B' and (resid 575 through 596 )
26X-RAY DIFFRACTION26chain 'B' and (resid 597 through 661 )
27X-RAY DIFFRACTION27chain 'B' and (resid 662 through 675 )
28X-RAY DIFFRACTION28chain 'B' and (resid 676 through 697 )
29X-RAY DIFFRACTION29chain 'B' and (resid 698 through 722 )
30X-RAY DIFFRACTION30chain 'B' and (resid 723 through 748 )
31X-RAY DIFFRACTION31chain 'B' and (resid 749 through 762 )
32X-RAY DIFFRACTION32chain 'C' and (resid 1 through 3 )

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