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- PDB-2nut: Crystal Structure of the human Sec23a/24a heterodimer, complexed ... -

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Basic information

Entry
Database: PDB / ID: 2nut
TitleCrystal Structure of the human Sec23a/24a heterodimer, complexed with the SNARE protein Sec22b
Components
  • Protein transport protein Sec23AProtein targeting
  • Protein transport protein Sec24AProtein targeting
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / Human COPII Sec23-24 complexed with Sec22
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / transport vesicle / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / cholesterol homeostasis / protein localization to plasma membrane / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / phagocytic vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / ER-Phagosome pathway / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal ...Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / 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 / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / Beta-Lactamase / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMancias, J.D. / Goldberg, J.
CitationJournal: Mol.Cell / Year: 2007
Title: The Transport Signal on Sec22 for Packaging into COPII-Coated Vesicles is a Conformational Epitope
Authors: Mancias, J.D. / Goldberg, J.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 Sec24A
C: Vesicle-trafficking protein SEC22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,0615
Polymers193,9303
Non-polymers1312
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-15 kcal/mol
Surface area66150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.280, 97.580, 129.800
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 86551.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Production host: Hi5 insect cells / References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / Protein targeting / SEC24-related protein A


Mass: 84961.578 Da / Num. of mol.: 1 / Fragment: Sec24a fragment lacking n-terminal residues 1-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Production host: Hi5 insect cells / References: UniProt: O95486
#3: Protein Vesicle-trafficking protein SEC22b / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1 / ERS24 / ERS- 24


Mass: 22416.590 Da / Num. of mol.: 1 / Fragment: Sec22b cytosolic domain, residues 1-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC22B, SEC22L1 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: O75396
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 10% (w/v) PEG 4000, 0.5M sodium acetate and 50 mM Tris buffer, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2005
Details: Mirror: Platinum-coated 1:1 focusing toroidal mirror
RadiationMonochromator: Double silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 77749 / % possible obs: 94.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.061 / Χ2: 1.43 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.1 / Num. unique all: 7880 / Rsym value: 0.268 / Χ2: 1.098 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NUP

2nup


Resolution: 2.3→30 Å / FOM work R set: 0.795 / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3747 4.6 %RANDOM
Rwork0.219 ---
obs-73609 89.5 %-
Solvent computationBsol: 43.746 Å2
Displacement parametersBiso mean: 47.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.208 Å20 Å27.691 Å2
2--2.452 Å20 Å2
3----2.659 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12475 0 2 301 12778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.385
X-RAY DIFFRACTIONc_mcbond_it3.7223.5
X-RAY DIFFRACTIONc_scbond_it5.144
X-RAY DIFFRACTIONc_mcangle_it5.2554
X-RAY DIFFRACTIONc_scangle_it6.7284.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.320.325840.3112841368
2.32-2.330.424650.31512771342
2.33-2.350.361590.31313151374
2.35-2.360.393680.31512171285
2.36-2.380.379680.29213661434
2.38-2.40.315600.28713281388
2.4-2.420.353560.30213101366
2.42-2.440.379750.28713271402
2.44-2.460.354650.28913841449
2.46-2.480.374680.30613491417
2.48-2.50.339590.27514231482
2.5-2.520.324770.2713751452
2.52-2.540.299830.27313941477
2.54-2.570.373670.28213631430
2.57-2.590.308820.27514161498
2.59-2.620.312790.26414231502
2.62-2.640.3750.26613631438
2.64-2.670.398860.29214011487
2.67-2.70.289700.25513941464
2.7-2.730.359620.26714011463
2.73-2.760.341840.26614301514
2.76-2.790.297550.27414221477
2.79-2.820.336750.26414261501
2.82-2.860.361820.27214891571
2.86-2.90.32730.25113891462
2.9-2.940.313900.23514091499
2.94-2.980.329760.24114701546
2.98-3.020.297830.23914251508
3.02-3.070.304880.23114651553
3.07-3.120.32680.24514601528
3.12-3.170.289850.22414911576
3.17-3.230.266920.21514461538
3.23-3.290.251760.20414761552
3.29-3.360.287790.21614761555
3.36-3.430.263790.21214731552
3.43-3.510.254780.21614531531
3.51-3.60.2721100.20414751585
3.6-3.70.236810.20514581539
3.7-3.810.232830.19914391522
3.81-3.930.217900.18314571547
3.93-4.070.183720.16714431515
4.07-4.230.188780.16414651543
4.23-4.430.196730.16114181491
4.43-4.660.234770.16914271504
4.66-4.950.195920.17313961488
4.95-5.330.296760.19914171493
5.33-5.860.24670.21914481515
5.86-6.70.258610.20414151476
6.7-8.410.237740.19213901464
8.41-300.253420.219904946
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5zinc.parzinc.top

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