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- PDB-6h9m: Coiled-coil domain-containing protein 90B residues 43-125 from Ho... -

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Basic information

Entry
Database: PDB / ID: 6h9m
TitleCoiled-coil domain-containing protein 90B residues 43-125 from Homo sapiens fused to a GCN4 adaptor
ComponentsCoiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4
KeywordsMEMBRANE PROTEIN / coiled coil / beta-layer / mitochondrial membrane
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / mitochondrial membrane / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding / nucleus
Similarity search - Function
Coiled-coil domain-containing protein 90-like / Coiled-coil domain-containing protein 90-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily ...Coiled-coil domain-containing protein 90-like / Coiled-coil domain-containing protein 90-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Coiled-coil domain-containing protein 90B, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAdlakha, J. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D.
CitationJournal: Structure / Year: 2019
Title: Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles.
Authors: Adlakha, J. / Karamichali, I. / Sangwallek, J. / Deiss, S. / Bar, K. / Coles, M. / Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionAug 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Coiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4
B: Coiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4
C: Coiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)40,7093
Polymers40,7093
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-105 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.009, 298.178, 29.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 62 - 155 / Label seq-ID: 23 - 116

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Coiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 13569.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CCDC90B, CUA003, MDS011, MDS025, GCN4, AAS3, ARG9, YEL009C
Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZT6, UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: Molecular Dimensions Morpheus Screen, Well F2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0703 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0703 Å / Relative weight: 1
ReflectionResolution: 2.1→37.3 Å / Num. obs: 19522 / % possible obs: 99.8 % / Redundancy: 6.27 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.46 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.89 / CC1/2: 0.835 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5APQ

5apq


Resolution: 2.1→37.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 15.664 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25728 976 5 %RANDOM
Rwork0.23095 ---
obs0.23239 18543 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20 Å2
2---5.49 Å20 Å2
3---6.44 Å2
Refinement stepCycle: 1 / Resolution: 2.1→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 0 55 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192277
X-RAY DIFFRACTIONr_bond_other_d0.0060.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.963075
X-RAY DIFFRACTIONr_angle_other_deg1.26535235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8415279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68326.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02215456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.935156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02468
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.54515.3771125
X-RAY DIFFRACTIONr_mcbond_other10.5515.3711124
X-RAY DIFFRACTIONr_mcangle_it13.58725.8151401
X-RAY DIFFRACTIONr_mcangle_other13.58225.8291402
X-RAY DIFFRACTIONr_scbond_it15.22717.9911151
X-RAY DIFFRACTIONr_scbond_other15.2217.9981152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other17.32928.8551674
X-RAY DIFFRACTIONr_long_range_B_refined19.57570.1242598
X-RAY DIFFRACTIONr_long_range_B_other19.60270.032587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A46140.16
12B46140.16
21A46170.17
22C46170.17
31B45910.16
32C45910.16
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 66 -
Rwork0.386 1269 -
obs--97.37 %
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)
11.4682-3.38981.00213.1245-4.8091.8817-0.3623-0.0950.55230.64140.3496-0.6923-0.1936-0.07770.01270.8202-0.0196-0.05770.6463-0.09260.6039-6.5504138.324718.1713
22.47750.2569-0.938414.49487.69694.5615-0.14630.53620.0703-0.2261-0.11520.6478-0.0862-0.28150.26150.73310.0518-0.01490.4641-0.01770.4223-19.2553141.34755.0675
313.5499-12.6676-5.442511.87615.17552.41740.56130.52740.4069-0.5867-0.3446-0.381-0.31770.2251-0.21670.9905-0.07130.11130.86830.08670.9972-1.2917140.52380.7969
41.1340.76650.9537.45772.85491.527-0.0852-0.2140.044-0.2334-0.03150.1634-0.2054-0.13190.11670.41140.00090.0060.2523-0.01860.262-15.3489129.144710.0985
50.9859-2.0909-0.49799.11793.18711.23250.0608-0.06920.1817-0.306-0.0689-0.2093-0.1812-0.05980.00810.53330.03370.0260.30940.02510.3163-9.946130.37680.0793
61.22424.0081-0.219515.678-0.74670.14610.1174-0.00970.25950.1723-0.1086-0.0637-0.18060.1756-0.00880.5239-0.0821-0.02260.40740.01330.4151-3.7209128.18349.3511
70.7951-2.4944-0.638516.48834.20981.1486-0.0389-0.0024-0.04470.07610.03960.08880.0445-0.0006-0.00070.0108-0.0083-0.00610.1320.02190.0129-10.664471.9128-0.6778
80.23850.6787-0.12858.74660.95520.4799-0.02860.0288-0.0223-0.2512-0.04260.0834-0.0523-0.02580.07120.03350.0034-0.04070.17740.00640.0739-16.126973.7506-7.303
90.30171.23620.534214.46434.87492.2243-0.02820.0505-0.0212-0.3030.066-0.1493-0.0265-0.0129-0.03780.0189-0.00240.01060.16280.02380.0332-7.748673.3614-8.8601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2B1 - 76
3X-RAY DIFFRACTION3C1 - 76
4X-RAY DIFFRACTION4A77 - 101
5X-RAY DIFFRACTION5B77 - 101
6X-RAY DIFFRACTION6C77 - 101
7X-RAY DIFFRACTION7A102 - 333
8X-RAY DIFFRACTION8B102 - 333
9X-RAY DIFFRACTION9C102 - 333

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