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- PDB-2qc7: Crystal structure of the protein-disulfide isomerase related chap... -

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Basic information

Entry
Database: PDB / ID: 2qc7
TitleCrystal structure of the protein-disulfide isomerase related chaperone ERp29
ComponentsEndoplasmic reticulum protein ERp29
KeywordsCHAPERONE / b domain (residues 33-153) / D domain (residues 154-261)
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / protein unfolding / smooth endoplasmic reticulum / negative regulation of protein secretion / transport vesicle / intracellular protein transport / positive regulation of MAP kinase activity / melanosome / protein folding ...regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / protein unfolding / smooth endoplasmic reticulum / negative regulation of protein secretion / transport vesicle / intracellular protein transport / positive regulation of MAP kinase activity / melanosome / protein folding / protein-folding chaperone binding / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of gene expression / cell surface / endoplasmic reticulum / protein homodimerization activity / membrane
Similarity search - Function
Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin ...Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBarak, N.N. / Sevvana, M. / Neumann, P. / Malesevic, M. / Naumann, K. / Fischer, G. / Sheldrick, G.M. / Stubbs, M.T. / Ferrari, D.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure and functional analysis of the protein disulfide isomerase-related protein ERp29.
Authors: Barak, N.N. / Neumann, P. / Sevvana, M. / Schutkowski, M. / Naumann, K. / Malesevic, M. / Reichardt, H. / Fischer, G. / Stubbs, M.T. / Ferrari, D.M.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Endoplasmic reticulum protein ERp29
B: Endoplasmic reticulum protein ERp29


Theoretical massNumber of molelcules
Total (without water)54,4442
Polymers54,4442
Non-polymers00
Water0
1
A: Endoplasmic reticulum protein ERp29

A: Endoplasmic reticulum protein ERp29


Theoretical massNumber of molelcules
Total (without water)54,4442
Polymers54,4442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Endoplasmic reticulum protein ERp29

B: Endoplasmic reticulum protein ERp29


Theoretical massNumber of molelcules
Total (without water)54,4442
Polymers54,4442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)58.044, 68.025, 70.088
Angle α, β, γ (deg.)90.00, 107.46, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
371A
381B
391A
401B
411A
421B
431A
441B
451A
461B
471A
481B
491A
501B
511A
521B
531A
541B
551A
561B
571A
581B
591A
601B
611A
621B
631A
641B
651A
661B
671A
681B
691A
701B
12A
22B
32A
42B
52A
62B
72A
82B
92A
102B
112A
122B
132A
142B
152A
162B
172A
182B
192A
202B
212A
222B
232A
242B
252A
262B
272A
282B
292A
302B
312A
322B
332A
342B
352A
362B
372A
382B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALLYSLYS6AA33 - 362 - 5
211VALVALLYSLYS6BB33 - 362 - 5
321GLYGLYTYRTYR1AA37 - 476 - 16
421GLYGLYTYRTYR1BB37 - 476 - 16
531LYSLYSLYSLYS3AA4817
631LYSLYSLYSLYS3BB4817
741VALVALLYSLYS1AA49 - 5218 - 21
841VALVALLYSLYS1BB49 - 5218 - 21
951LYSLYSLYSLYS3AA5423
1051LYSLYSLYSLYS3BB5423
1161PHEPHEVALVAL1AA55 - 5824 - 27
1261PHEPHEVALVAL1BB55 - 5824 - 27
1371TYRTYRLYSLYS6AA66 - 6935 - 38
1471TYRTYRLYSLYS6BB66 - 6935 - 38
1581GLNGLNPHEPHE1AA70 - 7339 - 42
1681GLNGLNPHEPHE1BB70 - 7339 - 42
1791ASPASPTYRTYR6AA95 - 9664 - 65
1891ASPASPTYRTYR6BB95 - 9664 - 65
19101GLYGLYASPASP1AA97 - 9866 - 67
20101GLYGLYASPASP1BB97 - 9866 - 67
21111LEULEULEULEU3AA10069
22111LEULEULEULEU3BB10069
23121ASNASNASNASN1AA10170
24121ASNASNASNASN1BB10170
25131ASPASPASPASP1AA11180
26131ASPASPASPASP1BB11180
27141SERSERPHEPHE1AA114 - 12183 - 90
28141SERSERPHEPHE1BB114 - 12183 - 90
29151ARGARGARGARG3AA12291
30151ARGARGARGARG3BB12291
31161ASPASPTYRTYR1AA123 - 13292 - 101
32161ASPASPTYRTYR1BB123 - 13292 - 101
33171LYSLYSLYSLYS3AA137106
34171LYSLYSLYSLYS3BB137106
35181VALVALGLNGLN1AA138 - 142107 - 111
36181VALVALGLNGLN1BB138 - 142107 - 111
37191ARGARGARGARG3AA170139
38191ARGARGARGARG3BB170139
39201ALAALAVALVAL1AA171 - 174140 - 143
40201ALAALAVALVAL1BB171 - 174140 - 143
41211GLUGLUARGARG3AA175 - 177144 - 146
42211GLUGLUARGARG3BB175 - 177144 - 146
43221GLNGLNLEULEU1AA178 - 181147 - 150
44221GLNGLNLEULEU1BB178 - 181147 - 150
45231LYSLYSGLNGLN3AA182 - 185151 - 154
46231LYSLYSGLNGLN3BB182 - 185151 - 154
47241SERSERSERSER3AA189158
48241SERSERSERSER3BB189158
49251SERSERLYSLYS1AA190 - 192159 - 161
50251SERSERLYSLYS1BB190 - 192159 - 161
51261LYSLYSGLYGLY1AA197 - 213166 - 182
52261LYSLYSGLYGLY1BB197 - 213166 - 182
53271GLUGLUASPASP6AA214 - 215183 - 184
54271GLUGLUASPASP6BB214 - 215183 - 184
55281PHEPHEILEILE1AA216 - 228185 - 197
56281PHEPHEILEILE1BB216 - 228185 - 197
57291GLUGLULYSLYS3AA229 - 230198 - 199
58291GLUGLULYSLYS3BB229 - 230198 - 199
59301ASNASNGLYGLY1AA231 - 236200 - 205
60301ASNASNGLYGLY1BB231 - 236200 - 205
61311LYSLYSLYSLYS3AA237206
62311LYSLYSLYSLYS3BB237206
63321LYSLYSGLUGLU1AA238 - 239207 - 208
64321LYSLYSGLUGLU1BB238 - 239207 - 208
65331GLUGLUGLUGLU3AA240209
66331GLUGLUGLUGLU3BB240209
67341LEULEUPHEPHE1AA241 - 251210 - 220
68341LEULEUPHEPHE1BB241 - 251210 - 220
69351GLNGLNALAALA6AA252 - 256221 - 225
70351GLNGLNALAALA6BB252 - 256221 - 225
112LYSLYSLYSLYS3AA5928
212LYSLYSLYSLYS3BB5928
322PHEPHEPROPRO1AA60 - 6529 - 34
422PHEPHEPROPRO1BB60 - 6529 - 34
532LYSLYSLYSLYS3AA7443
632LYSLYSLYSLYS3BB7443
742ARGARGSERSER1AA75 - 9444 - 63
842ARGARGSERSER1BB75 - 9444 - 63
952LYSLYSLYSLYS3AA9968
1052LYSLYSLYSLYS3BB9968
1162METMETGLUGLU3AA102 - 10371 - 72
1262METMETGLUGLU3BB102 - 10371 - 72
1372LEULEUGLUGLU1AA104 - 10673 - 75
1472LEULEUGLUGLU1BB104 - 10673 - 75
1582LYSLYSLYSLYS3AA10776
1682LYSLYSLYSLYS3BB10776
1792TYRTYRTYRTYR1AA10877
1892TYRTYRTYRTYR1BB10877
19102LYSLYSLEULEU3AA109 - 11078 - 79
20102LYSLYSLEULEU3BB109 - 11078 - 79
21112LYSLYSGLUGLU3AA112 - 11381 - 82
22112LYSLYSGLUGLU3BB112 - 11381 - 82
23122THRTHRTHRTHR3AA133102
24122THRTHRTHRTHR3BB133102
25132GLYGLYVALVAL1AA134 - 136103 - 105
26132GLYGLYVALVAL1BB134 - 136103 - 105
27142ARGARGARGARG3AA143112
28142ARGARGARGARG3BB143112
29152TRPTRPLEULEU1AA144 - 145113 - 114
30152TRPTRPLEULEU1BB144 - 145113 - 114
31162LYSLYSLYSLYS3AA146115
32162LYSLYSLYSLYS3BB146115
33172GLYGLYPHEPHE1AA147 - 168116 - 137
34172GLYGLYPHEPHE1BB147 - 168116 - 137
35182ASPASPLEULEU6AA186 - 188155 - 157
36182ASPASPLEULEU6BB186 - 188155 - 157
37192GLUGLULYSLYS3AA193 - 196162 - 165
38192GLUGLULYSLYS3BB193 - 196162 - 165

NCS ensembles :
ID
1
2

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Components

#1: Protein Endoplasmic reticulum protein ERp29 / / ERp31 / ERp28


Mass: 27222.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERP29, C12orf8, ERP28 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P30040

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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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10 mg/ml protein in 5 mM HEPES, pH 7.5, 25 mM NaCl, 0.0025% (v/v) beta-mercaptoethanol was equlibrated with a reservoir containing 0.45 M (NH4)2SO4, 0.1 M sodium acetate buffer, pH 4.5 and ...Details: 10 mg/ml protein in 5 mM HEPES, pH 7.5, 25 mM NaCl, 0.0025% (v/v) beta-mercaptoethanol was equlibrated with a reservoir containing 0.45 M (NH4)2SO4, 0.1 M sodium acetate buffer, pH 4.5 and 18-20% (w/v) PEG 2000 monomethyl ether. Crystals of about 0.1 mm in size grew in two days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.96676 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96676 Å / Relative weight: 1
ReflectionResolution: 2.9→28.981 Å / Num. obs: 11070 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 89.5 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.065.90.5991.31005517120.599100
3.06-3.245.90.3482.2923115750.348100
3.24-3.475.90.2283.2766412990.22885.1
3.47-3.745.90.1375.3702111940.13785
3.74-4.15.80.0917.7651711160.09186.1
4.1-4.595.80.06111678111600.061100
4.59-5.295.90.05512621110580.055100
5.29-6.485.80.06310.751468870.063100
6.48-9.175.80.04613.339456840.046100
9.17-29.985.40.03416.220913850.03496.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å29.98 Å
Translation2.9 Å29.98 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OVN
Resolution: 2.9→28.98 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.913 / SU B: 65.046 / SU ML: 0.536 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used NCS restraines and TLS refinement. 4 TLS groups were used, 2 for each of the monomers (one for b and d domain respectively.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 560 5.1 %RANDOM
Rwork0.265 ---
all0.265 11701 --
obs0.265 11068 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å27.49 Å2
2---3.12 Å20 Å2
3---7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.486 Å-
Luzzati d res low-6 Å
Luzzati sigma a0.536 Å-
Refinement stepCycle: LAST / Resolution: 2.9→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 0 0 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223598
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9874838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0665444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.03325.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72615674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3281514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022690
X-RAY DIFFRACTIONr_nbd_refined0.3460.32145
X-RAY DIFFRACTIONr_nbtor_refined0.3610.52529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2930.5275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3910.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.57
X-RAY DIFFRACTIONr_mcbond_it0.77122262
X-RAY DIFFRACTIONr_mcangle_it1.27233542
X-RAY DIFFRACTIONr_scbond_it0.68421515
X-RAY DIFFRACTIONr_scangle_it1.08331296
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1939TIGHT POSITIONAL0.020.02
1225LOOSE POSITIONAL1.55
1939TIGHT THERMAL0.10.5
1225LOOSE THERMAL1.7510
2493TIGHT POSITIONAL0.020.02
294LOOSE POSITIONAL0.995
2493TIGHT THERMAL0.130.5
294LOOSE THERMAL1.4910
LS refinement shellResolution: 2.9→3.055 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 85 -
Rwork0.382 1612 -
obs-1697 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
112.11180.9623-2.17993.7368-0.05115.72620.0946-1.31980.04450.4588-0.0649-0.0631-0.35740.3596-0.0298-0.1921-0.008-0.0363-0.00810.0082-0.36599.94233.57666.3168
24.17081.5385-0.444615.60811.56565.89480.06220.46440.4412-1.6879-0.0876-0.0571-0.12110.24840.02540.32120.06410.0406-0.12210.0869-0.080622.7622-1.9323-22.571
38.00890.3399-3.30444.38410.02318.21420.17450.7299-0.058-0.430.01130.7535-0.209-0.902-0.18570.21270.1098-0.06390.04680.0168-0.183313.883635.712522.7343
46.08751.40070.349919.48333.12683.5287-0.19940.31060.02980.66910.248-1.23120.20220.3382-0.04860.24160.1237-0.0052-0.12050.097-0.065244.204941.394814.347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 1542 - 123
2X-RAY DIFFRACTION2AA155 - 256124 - 225
3X-RAY DIFFRACTION3BB33 - 1542 - 123
4X-RAY DIFFRACTION4BB155 - 256124 - 225

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