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- PDB-3qca: Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Do... -

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Basic information

Entry
Database: PDB / ID: 3qca
TitleCrystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Domain Reveals The Conserved FcisP Touch-Turn Motif of UBX Domain Suffering Conformational Change
ComponentsFAS-associated factor 1
KeywordsPROTEIN BINDING / UBX / FAF1
Function / homology
Function and homology information


ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / ERAD pathway ...ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / ERAD pathway / heat shock protein binding / positive regulation of DNA replication / ubiquitin binding / positive regulation of protein-containing complex assembly / positive regulation of protein catabolic process / nuclear envelope / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of apoptotic process / protein domain specific binding / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. ...: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, K.H. / Kang, W. / Suh, S.W. / Yang, J.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of human FAF1 UBX domain reveals a novel FcisP touch-turn motif in p97/VCP-binding region
Authors: Kang, W. / Yang, J.K.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAS-associated factor 1
B: FAS-associated factor 1
C: FAS-associated factor 1
D: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)39,3414
Polymers39,3414
Non-polymers00
Water55831
1
A: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,8351
Polymers9,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,8351
Polymers9,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,8351
Polymers9,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,8351
Polymers9,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.730, 175.730, 175.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25B
35C
45D
16A
26B
36C
46D
17A
27B
37C
47D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPHEPHE3AA573 - 6087 - 42
21VALVALPHEPHE3BB573 - 6087 - 42
31VALVALPHEPHE3CC573 - 6087 - 42
41VALVALPHEPHE3DD573 - 6087 - 42
12PROPROASPASP6AA609 - 61143 - 45
22PROPROASPASP6BB609 - 61143 - 45
32PROPROASPASP6CC609 - 61143 - 45
42PROPROASPASP6DD609 - 61143 - 45
13GLUGLULEULEU3AA612 - 61646 - 50
23GLUGLULEULEU3BB612 - 61646 - 50
33GLUGLULEULEU3CC612 - 61646 - 50
43GLUGLULEULEU3DD612 - 61646 - 50
14SERSERARGARG6AA617 - 62151 - 55
24SERSERARGARG6BB617 - 62151 - 55
34SERSERARGARG6CC617 - 62151 - 55
44SERSERARGARG6DD617 - 62151 - 55
15ARGARGLYSLYS3AA622 - 63756 - 71
25ARGARGLYSLYS3BB622 - 63756 - 71
35ARGARGLYSLYS3CC622 - 63756 - 71
45ARGARGLYSLYS3DD622 - 63756 - 71
16LEULEUPROPRO6AA638 - 64072 - 74
26LEULEUPROPRO6BB638 - 64072 - 74
36LEULEUPROPRO6CC638 - 64072 - 74
46LEULEUPROPRO6DD638 - 64072 - 74
17GLNGLNALAALA3AA641 - 64875 - 82
27GLNGLNALAALA3BB641 - 64875 - 82
37GLNGLNALAALA3CC641 - 64875 - 82
47GLNGLNALAALA3DD641 - 64875 - 82

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 9835.250 Da / Num. of mol.: 4 / Fragment: UBX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M Ammonium Sulfate, 0.1M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.555
11-K, -H, -L20.445
ReflectionResolution: 2.9→30 Å / Num. all: 10089 / Num. obs: 10089 / % possible obs: 99.9 %
Reflection shellResolution: 2.9→3.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.855 / SU B: 35.995 / SU ML: 0.623 / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29261 487 4.8 %RANDOM
Rwork0.24675 ---
all0.24886 9593 --
obs0.24886 9593 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.56 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 0 31 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9923540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92223.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.48815436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2691518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211988
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4141.51616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79122610
X-RAY DIFFRACTIONr_scbond_it0.9153992
X-RAY DIFFRACTIONr_scangle_it1.7034.5930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A144TIGHT POSITIONAL0.040.05
1B144TIGHT POSITIONAL0.040.05
1C144TIGHT POSITIONAL0.040.05
1D144TIGHT POSITIONAL0.040.05
1A136LOOSE POSITIONAL0.055
1B136LOOSE POSITIONAL0.045
1C136LOOSE POSITIONAL0.045
1D136LOOSE POSITIONAL0.055
1A144TIGHT THERMAL0.070.5
1B144TIGHT THERMAL0.060.5
1C144TIGHT THERMAL0.060.5
1D144TIGHT THERMAL0.080.5
1A136LOOSE THERMAL0.0710
1B136LOOSE THERMAL0.0610
1C136LOOSE THERMAL0.0610
1D136LOOSE THERMAL0.0810
2A29LOOSE POSITIONAL0.965
2B29LOOSE POSITIONAL0.735
2C29LOOSE POSITIONAL0.655
2D29LOOSE POSITIONAL0.915
2A29LOOSE THERMAL2.2310
2B29LOOSE THERMAL0.5310
2C29LOOSE THERMAL0.910
2D29LOOSE THERMAL1.5310
3A20TIGHT POSITIONAL0.020.05
3B20TIGHT POSITIONAL0.050.05
3C20TIGHT POSITIONAL0.030.05
3D20TIGHT POSITIONAL0.030.05
3A22LOOSE POSITIONAL0.095
3B22LOOSE POSITIONAL0.075
3C22LOOSE POSITIONAL0.055
3D22LOOSE POSITIONAL0.075
3A20TIGHT THERMAL0.070.5
3B20TIGHT THERMAL0.070.5
3C20TIGHT THERMAL0.080.5
3D20TIGHT THERMAL0.060.5
3A22LOOSE THERMAL0.0610
3B22LOOSE THERMAL0.0610
3C22LOOSE THERMAL0.0510
3D22LOOSE THERMAL0.0710
4A31LOOSE POSITIONAL1.095
4B31LOOSE POSITIONAL0.935
4C31LOOSE POSITIONAL1.315
4D31LOOSE POSITIONAL1.045
4A31LOOSE THERMAL1.1310
4B31LOOSE THERMAL2.3210
4C31LOOSE THERMAL1.9510
4D31LOOSE THERMAL3.3110
5A44TIGHT POSITIONAL0.030.05
5B44TIGHT POSITIONAL0.040.05
5C44TIGHT POSITIONAL0.030.05
5D44TIGHT POSITIONAL0.040.05
5A40LOOSE POSITIONAL0.055
5B40LOOSE POSITIONAL0.045
5C40LOOSE POSITIONAL0.045
5D40LOOSE POSITIONAL0.055
5A44TIGHT THERMAL0.070.5
5B44TIGHT THERMAL0.060.5
5C44TIGHT THERMAL0.050.5
5D44TIGHT THERMAL0.070.5
5A40LOOSE THERMAL0.0610
5B40LOOSE THERMAL0.0610
5C40LOOSE THERMAL0.0710
5D40LOOSE THERMAL0.0510
6A15LOOSE POSITIONAL0.245
6B15LOOSE POSITIONAL0.225
6C15LOOSE POSITIONAL0.185
6D15LOOSE POSITIONAL0.135
6A15LOOSE THERMAL3.3710
6B15LOOSE THERMAL1.0110
6C15LOOSE THERMAL0.6910
6D15LOOSE THERMAL4.1410
7A32TIGHT POSITIONAL0.030.05
7B32TIGHT POSITIONAL0.030.05
7C32TIGHT POSITIONAL0.020.05
7D32TIGHT POSITIONAL0.020.05
7A34LOOSE POSITIONAL0.045
7B34LOOSE POSITIONAL0.045
7C34LOOSE POSITIONAL0.025
7D34LOOSE POSITIONAL0.025
7A32TIGHT THERMAL0.060.5
7B32TIGHT THERMAL0.060.5
7C32TIGHT THERMAL0.040.5
7D32TIGHT THERMAL0.040.5
7A34LOOSE THERMAL0.0610
7B34LOOSE THERMAL0.0410
7C34LOOSE THERMAL0.0310
7D34LOOSE THERMAL0.0310
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 26 -
Rwork0.362 710 -
obs--99.86 %

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