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- PDB-3qml: The structural analysis of Sil1-Bip complex reveals the mechanism... -

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Basic information

Entry
Database: PDB / ID: 3qml
TitleThe structural analysis of Sil1-Bip complex reveals the mechanism for Sil1 to function as a novel nucleotide exchange factor
Components
  • 78 kDa glucose-regulated protein homolog
  • Nucleotide exchange factor SIL1
KeywordsCHAPERONE/PROTEIN TRANSPORT / Armadillo like repeats / CHAPERONE-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / adenyl-nucleotide exchange factor activity / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation ...fungal-type cell wall beta-glucan biosynthetic process / detection of unfolded protein / luminal surveillance complex / ubiquitin-dependent glycoprotein ERAD pathway / karyogamy involved in conjugation with cellular fusion / protein localization to endoplasmic reticulum / endoplasmic reticulum chaperone complex / adenyl-nucleotide exchange factor activity / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Nucleotide exchange factor Sil1, fungi / Nucleotide exchange factor SIL1 / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site ...Nucleotide exchange factor Sil1, fungi / Nucleotide exchange factor SIL1 / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Armadillo-like helical / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endoplasmic reticulum chaperone BiP / Nucleotide exchange factor SIL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsYan, M. / Li, J.Z. / Sha, B.D.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor.
Authors: Yan, M. / Li, J. / Sha, B.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: 78 kDa glucose-regulated protein homolog
B: 78 kDa glucose-regulated protein homolog
C: Nucleotide exchange factor SIL1
D: Nucleotide exchange factor SIL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,13915
Polymers158,3074
Non-polymers83311
Water3,711206
1
A: 78 kDa glucose-regulated protein homolog
C: Nucleotide exchange factor SIL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6069
Polymers79,1532
Non-polymers4537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein homolog
D: Nucleotide exchange factor SIL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5336
Polymers79,1532
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)226.353, 116.586, 55.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 78 kDa glucose-regulated protein homolog / GRP-78 / Immunoglobulin heavy chain-binding protein homolog / BiP


Mass: 42453.094 Da / Num. of mol.: 2 / Fragment: unp residues 43-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KAR2, GRP78, SSD1, YJL034W, J1248 / Production host: Escherichia coli (E. coli) / References: UniProt: P16474
#2: Protein Nucleotide exchange factor SIL1 / Protein SLS1


Mass: 36700.289 Da / Num. of mol.: 2 / Fragment: unp residues 113-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIL1, PER100, SLS1, YOL031C / Production host: Escherichia coli (E. coli) / References: UniProt: Q08199
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 100 mM HEPES buffer, 25% (w/v) PEG4K, 0.2 M Ammonium sulfate, pH 7.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.978 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 3, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 60106 / Num. obs: 60106 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 79.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_351)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→46.129 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3052 5.08 %RANDOM
Rwork0.2102 ---
obs0.2133 60106 91.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.692 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2151 Å20 Å20 Å2
2--6.441 Å2-0 Å2
3---1.7742 Å2
Refinement stepCycle: LAST / Resolution: 2.31→46.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10129 0 43 206 10378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810306
X-RAY DIFFRACTIONf_angle_d1.09813897
X-RAY DIFFRACTIONf_dihedral_angle_d16.3063882
X-RAY DIFFRACTIONf_chiral_restr0.0721594
X-RAY DIFFRACTIONf_plane_restr0.0041792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3124-2.3950.35962620.28584563X-RAY DIFFRACTION75
2.395-2.49090.32872600.25375032X-RAY DIFFRACTION82
2.4909-2.60430.31122610.24615221X-RAY DIFFRACTION84
2.6043-2.74160.34473000.24835433X-RAY DIFFRACTION88
2.7416-2.91330.33053220.24055678X-RAY DIFFRACTION92
2.9133-3.13820.3173400.23775933X-RAY DIFFRACTION96
3.1382-3.45390.31072960.2346169X-RAY DIFFRACTION99
3.4539-3.95350.2573250.19236191X-RAY DIFFRACTION99
3.9535-4.980.21763350.16926282X-RAY DIFFRACTION99
4.98-46.13850.23013510.18786552X-RAY DIFFRACTION100
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)
10.81320.01290.38791.11290.87140.6875-0.02790.0786-0.01210.05390.03970.01450.03180.0161-0.00890.2064-0.0210.01410.1880.05840.127431.868365.929362.6351
26.7224-0.45073.54450.3176-0.50581.86120.49221.5482-0.745-0.0892-0.04930.15560.16030.8126-0.42820.16480.1489-0.0370.45-0.17180.36066.602227.756835.5221
31.67940.63991.13321.19710.21111.7622-0.0324-0.02910.1388-0.11310.0370.147-0.16570.04850.00730.2971-0-0.03080.2235-0.02850.285835.931497.848177.903
43.2508-1.6358-0.99782.3077-0.49410.85810.48730.4675-0.2365-0.1123-0.29410.0694-0.075-0.1755-0.07340.29550.08130.01420.30950.0410.196339.503322.526948.8011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 48:424)
2X-RAY DIFFRACTION2(chain B and resid 48:425)
3X-RAY DIFFRACTION3(chain C and resid 122:406)
4X-RAY DIFFRACTION4(chain D and resid 125:406)

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