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- PDB-3uem: Crystal structure of human PDI bb'a' domains -

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Basic information

Entry
Database: PDB / ID: 3uem
TitleCrystal structure of human PDI bb'a' domains
ComponentsProtein disulfide-isomerase
KeywordsCHAPERONE / Protein disulfide isomerase / thioredoxin-like domain
Function / homology
Function and homology information


regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYu, J. / Wang, C. / Huo, L. / Feng, W. / Wang, C.-C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Human protein-disulfide isomerase is a redox-regulated chaperone activated by oxidation of domain a'
Authors: Wang, C. / Yu, J. / Huo, L. / Wang, L. / Feng, W. / Wang, C.-C.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 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: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9002
Polymers40,7481
Non-polymers1521
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.585, 76.076, 79.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein disulfide-isomerase / / PDI / Cellular thyroid hormone-binding protein / Prolyl 4-hydroxylase subunit beta / p55


Mass: 40747.781 Da / Num. of mol.: 1 / Fragment: bb'a' domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDI / Production host: Escherichia coli (E. coli) / References: UniProt: P07237, protein disulfide-isomerase
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25%(w/v) PEG3350, 0.1M Tris-HCl, 0.2M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 17802 / Num. obs: 17802 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 30.3
Reflection shellResolution: 2.29→2.38 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 17.744 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28031 906 5.1 %RANDOM
Rwork0.22302 ---
obs0.22585 16845 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.355 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 8 144 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222944
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.9533979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8495362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12525.315143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.619157
X-RAY DIFFRACTIONr_chiral_restr0.0720.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212240
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_it0.2991.51789
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55422886
X-RAY DIFFRACTIONr_scbond_it0.63831155
X-RAY DIFFRACTIONr_scangle_it1.0584.51090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.293→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 77 -
Rwork0.309 1195 -
obs--97.17 %
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)
116.43634.17490.991513.0469-12.801319.5173-0.0584-2.27841.12110.7383-0.15850.1282-0.9444-0.5160.21690.29060.1661-0.25670.2399-0.25760.2874-3.46053.9073-32.9595
26.78210.9766-1.61833.5914.21588.370.3179-0.1599-0.0272-0.0138-0.00990.4731-0.2997-0.3343-0.3080.15680.0669-0.0220.17760.07770.22760.0888-0.0196-24.1521
37.56141.0953-2.61766.3115-0.71639.43750.0527-0.17320.14960.1440.2901-0.16830.1040.5597-0.34280.17420.0589-0.03730.1721-0.00390.16527.725-0.0262-22.1714
46.68130.739-1.43199.05451.33699.23390.159-0.1371-0.72130.2430.0639-0.07330.78740.385-0.22290.17250.1238-0.0680.20590.02730.21367.4978-5.8482-22.6742
58.9344-0.4181-4.94839.9896-0.477518.06120.2494-0.32620.81320.34560.1033-0.1292-1.09490.325-0.35270.3432-0.00940.13380.08480.00180.26074.751110.4148-17.2889
65.46622.0374-6.01827.1626-4.612214.55960.5706-0.1314-0.0291.3496-0.1638-0.6708-0.78710.7122-0.40690.23620.0312-0.03460.1927-0.01390.05977.88752.3064-14.1236
78.075-0.5206-7.02386.97711.877919.96910.23-0.4020.15481.26590.1565-0.89730.26782.2979-0.38650.1810.0915-0.23470.2990.01150.105513.5205-3.8777-13.285
89.562112.1497-9.796421.3023-14.75213.82940.23261.0505-0.0058-0.302-0.41830.108-0.0871-0.45370.18570.4620.1767-0.140.3857-0.05830.10214.2058-14.1204-5.3783
938.4667.21230.9469.41330.2018-3.1429-0.63273.9265-0.8315-1.77110.5069-0.51430.27570.54340.12580.5457-0.05520.01210.7338-0.02470.11619.756-21.2654-4.4265
1011.43172.52690.595410.57863.57597.4786-0.0207-0.97090.63271.3956-0.55391.23030.0595-1.03320.57460.4224-0.12680.02720.3497-0.04010.09290.1845-13.506710.0085
118.86642.52734.01389.62913.62013.4740.21-0.2112-0.08240.3215-0.15910.56160.0754-0.3966-0.05090.3642-0.1371-0.10980.26470.04430.05882.3409-21.49655.3834
125.1763-0.27811.070111.6711.9816.67710.3714-0.5084-0.33341.4870.025-0.15810.8842-0.6929-0.39640.5087-0.289-0.17590.37820.13760.0926.7554-22.70413.2748
1313.0847-3.01411.941511.10661.75091.5667-0.1644-0.3548-0.33292.03220.5042-1.67920.28220.0065-0.33970.5888-0.1944-0.35330.19640.03530.253916.7697-18.792213.9148
149.77366.84145.676624.099.404914.69440.445-0.9137-0.34061.4844-0.65020.83350.4405-1.12310.20520.0533-0.0287-0.09010.1170.16290.06354.1659-48.256412.4397
157.1501-3.13434.99214.8817-3.60827.4336-0.1130.1396-0.25190.4502-0.0108-0.2984-0.04170.14830.12380.14820.0149-0.09850.16390.00420.198410.1525-47.08725.9574
1616.1207-13.32898.788111.1089-7.67227.89710.82270.3057-1.2007-0.7145-0.00380.3991.34220.4298-0.81890.17720.136-0.23560.1415-0.20740.33227.4187-57.2187-1.4824
176.2721-9.12360.79717.89432.49935.4543-0.16020.0617-0.09070.62270.2051-0.45870.0430.5415-0.0450.15280.0105-0.08270.22630.00620.21648.2451-45.51845.7167
185.0465-3.84210.77315.2612-2.8774.1893-0.07591.17130.15620.6573-0.5121-0.9153-0.30851.28110.58790.0376-0.0159-0.1570.4279-0.00320.276416.2536-42.79832.8039
195.7680.1476-0.82168.7724-0.504317.3182-0.21491.4572-0.7037-1.74740.6873-1.9662-0.60790.9865-0.47240.2440.15390.13820.7261-0.20980.421915.9614-50.3941-5.659
2011.1273-13.71740.09045.8789-1.139328.04170.33131.29350.5337-1.8145-0.0156-0.97021.04553.8051-0.31570.17530.3972-0.21670.892-0.27590.559120.7375-54.421-6.0384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A119 - 131
2X-RAY DIFFRACTION2A132 - 150
3X-RAY DIFFRACTION3A151 - 170
4X-RAY DIFFRACTION4A171 - 189
5X-RAY DIFFRACTION5A190 - 198
6X-RAY DIFFRACTION6A199 - 208
7X-RAY DIFFRACTION7A209 - 227
8X-RAY DIFFRACTION8A228 - 246
9X-RAY DIFFRACTION9A247 - 255
10X-RAY DIFFRACTION10A256 - 279
11X-RAY DIFFRACTION11A280 - 306
12X-RAY DIFFRACTION12A307 - 337
13X-RAY DIFFRACTION13A338 - 353
14X-RAY DIFFRACTION14A354 - 369
15X-RAY DIFFRACTION15A370 - 400
16X-RAY DIFFRACTION16A401 - 419
17X-RAY DIFFRACTION17A420 - 431
18X-RAY DIFFRACTION18A432 - 451
19X-RAY DIFFRACTION19A452 - 468
20X-RAY DIFFRACTION20A469 - 478

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