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- PDB-4u6u: Crystal Structure of the Cog5-Cog7 complex from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 4u6u
TitleCrystal Structure of the Cog5-Cog7 complex from Kluyveromyces lactis
Components
  • Cog5
  • Cog7
KeywordsTRANSPORT PROTEIN / multisubunit tethering complex / conserved oligomeric golgi complex / coiled coil / vesicle fusion
Function / homology
Function and homology information


Golgi transport complex / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2790 / Conserved oligomeric Golgi complex subunit 5 / Conserved oligomeric Golgi complex subunit 5, N-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Conserved oligomeric Golgi complex subunit 5 / KLLA0A08888p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsHa, J.Y. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex.
Authors: Ha, J.Y. / Pokrovskaya, I.D. / Climer, L.K. / Shimamura, G.R. / Kudlyk, T. / Jeffrey, P.D. / Lupashin, V.V. / Hughson, F.M.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cog7
B: Cog5
C: Cog7
D: Cog5


Theoretical massNumber of molelcules
Total (without water)82,6984
Polymers82,6984
Non-polymers00
Water0
1
A: Cog7
B: Cog5


Theoretical massNumber of molelcules
Total (without water)41,3492
Polymers41,3492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-23 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: Cog7
D: Cog5


Theoretical massNumber of molelcules
Total (without water)41,3492
Polymers41,3492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area18880 Å2
MethodPISA
3
A: Cog7
B: Cog5

C: Cog7
D: Cog5


Theoretical massNumber of molelcules
Total (without water)82,6984
Polymers82,6984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
Buried area9620 Å2
ΔGint-69 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)335.838, 335.838, 335.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROchain AAA8 - 745 - 71
21ALAALAPROPROchain CCC8 - 745 - 71
12GLNGLNASPASPchain BBB105 - 3868 - 289
22GLNGLNTHRTHRchain DDD105 - 3878 - 290

NCS ensembles :
ID
1
2
DetailsThe biological unit is a heterodimer. There are two biological units in the asymmetric unit (chains A+B, C+D).

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Components

#1: Protein Cog7


Mass: 8742.904 Da / Num. of mol.: 2 / Fragment: UNP residues 5-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0A08888g, KLLA0_A08888g / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CXE9
#2: Protein Cog5


Mass: 32606.244 Da / Num. of mol.: 2 / Fragment: UNP residues 99-387 / Mutation: E157A, E158A, E177A, E178A, E294A, E295A, E297A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0F03685g, KLLA0_F03685g / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CLE2

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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: 4.77 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 4000, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075, 0.9790, 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.9791
30.97921
ReflectionResolution: 3→50 Å / Num. obs: 33059 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 28.9 % / Biso Wilson estimate: 92.04 Å2 / Rsym value: 0.135 / Net I/σ(I): 26.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 29.6 % / Rmerge(I) obs: 2.285 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
CBASSdata collection
XDSdata scaling
SCALAdata scaling
SHARPphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→48.474 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 2425 7.36 %Random
Rwork0.1901 30544 --
obs0.1932 32969 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.12 Å2 / Biso mean: 111.6023 Å2 / Biso min: 43.51 Å2
Refinement stepCycle: final / Resolution: 3→48.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 0 0 5507
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015581
X-RAY DIFFRACTIONf_angle_d1.5037554
X-RAY DIFFRACTIONf_chiral_restr0.059910
X-RAY DIFFRACTIONf_plane_restr0.007967
X-RAY DIFFRACTIONf_dihedral_angle_d18.1732108
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A557X-RAY DIFFRACTION16.812TORSIONAL
12C557X-RAY DIFFRACTION16.812TORSIONAL
21B2545X-RAY DIFFRACTION16.812TORSIONAL
22D2545X-RAY DIFFRACTION16.812TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.06130.38841230.333817791902100
3.0613-3.12790.37011390.310617531892100
3.1279-3.20060.36921530.291617471900100
3.2006-3.28070.31361440.256717371881100
3.2807-3.36930.32271400.25517741914100
3.3693-3.46850.25621400.257217611901100
3.4685-3.58040.30561400.222917751915100
3.5804-3.70830.24991420.197217791921100
3.7083-3.85670.26971410.19817721913100
3.8567-4.03220.25211420.18917831925100
4.0322-4.24460.19791410.173417871928100
4.2446-4.51040.19781410.170317811922100
4.5104-4.85830.20121440.155818181962100
4.8583-5.34670.22291440.170218041948100
5.3467-6.11910.25161450.212218371982100
6.1191-7.70440.23461480.202918622010100
7.7044-48.48030.16841580.14591995215399
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)
13.73273.03193.47874.89744.50535.23490.6563-0.5540.29681.38950.37890.7846-1.93620.6242-0.65081.6829-0.06230.42440.7266-0.09830.746335.176854.09668.4116
25.0284-5.2751-3.11688.2471.06813.70780.2365-0.96632.41191.19780.3281-1.092-0.38282.2187-0.37821.1327-0.15290.1041.0738-0.33631.440646.139462.446564.9368
38.97066.23445.49045.2063.68474.3543-0.50551.7609-1.7773-1.12390.7995-1.16120.2130.5372-0.68090.63730.05140.09980.6366-0.20190.707932.671241.369651.671
43.43141.90471.20442.21252.51774.38440.23-0.60130.43330.0951-0.25141.1815-0.2547-0.1773-0.04950.63340.19330.14410.51450.04250.684429.554950.578758.0671
54.03921.3182-2.2924.2026-2.53523.4485-0.1802-0.01130.00520.7638-0.00910.1451-0.3971-0.20690.46081.7838-0.06090.51760.796-0.38051.53638.769280.612160.5936
61.6203-2.0023-1.37816.59362.82950.93620.07480.6305-0.3194-1.3208-0.3704-0.0854-0.2489-0.53850.30541.68110.0916-0.010.9528-0.24510.837923.6102111.142759.7334
74.5573-0.42960.80377.05750.79847.4706-0.927-0.8739-1.39971.45-0.21051.60611.2172-1.14440.69161.12190.01510.68480.45470.30971.708938.627221.975255.7102
81.44881.3215-2.21061.424-1.9183.4264-0.04270.6393-1.291-1.11150.01491.7610.9401-1.6610.14640.44780.174-0.14110.8355-0.44082.308536.125617.961939.1103
99.11831.18641.86514.36961.68844.5834-1.2768-0.43880.2897-0.21890.96861.027-1.41490.5940.41750.76410.10990.05830.45880.09510.530245.750737.923756.4535
104.86891.5803-0.13395.05471.71043.7374-0.8068-1.2721-0.63931.4710.63960.35670.91090.0134-0.07310.91270.31230.18010.73760.30210.812348.063330.484860.3396
114.8235-3.0215-3.8152.46340.78987.5748-0.73480.3457-0.65410.0608-0.12731.59861.5601-0.16020.82011.1592-0.0226-0.08760.4855-0.06041.225449.58047.940135.1136
122.1963-1.8178-0.64217.42042.09751.6668-0.12390.04850.02880.3013-0.14720.1824-0.0517-0.04380.260.78890.0498-0.05530.46060.05730.497572.6597-17.997923.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:37)A8 - 37
2X-RAY DIFFRACTION2(chain A and resid 38:50)A38 - 50
3X-RAY DIFFRACTION3(chain A and resid 51:74)A51 - 74
4X-RAY DIFFRACTION4(chain B and resid 105:140)B105 - 140
5X-RAY DIFFRACTION5(chain B and resid 141:191)B141 - 191
6X-RAY DIFFRACTION6(chain B and resid 192:386)B192 - 386
7X-RAY DIFFRACTION7(chain C and resid 8:37)C8 - 37
8X-RAY DIFFRACTION8(chain C and resid 38:44)C38 - 44
9X-RAY DIFFRACTION9(chain C and resid 45:74)C45 - 74
10X-RAY DIFFRACTION10(chain D and resid 105:137)D105 - 137
11X-RAY DIFFRACTION11(chain D and resid 138:200)D138 - 200
12X-RAY DIFFRACTION12(chain D and resid 201:387)D201 - 387

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