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- PDB-5jjm: Crystal Structure of Homodimeric Androgen Receptor Ligand-Binding... -

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Basic information

Entry
Database: PDB / ID: 5jjm
TitleCrystal Structure of Homodimeric Androgen Receptor Ligand-Binding Domain bound to DHT and LxxLL peptide
Components
  • (Androgen receptor) x 2
  • Unknown peptide
  • uba3-derived peptide
KeywordsTRANSCRIPTION / nuclear receptor / transcription factor / oxosteroid receptor / human androgen receptor
Function / homology
Function and homology information


E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / regulation of developmental growth / POU domain binding / positive regulation of integrin biosynthetic process ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / regulation of developmental growth / POU domain binding / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / cellular response to testosterone stimulus / regulation of systemic arterial blood pressure / Leydig cell differentiation / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / NEDD8 transferase activity / prostate gland epithelium morphogenesis / prostate gland growth / epithelial cell morphogenesis / membraneless organelle assembly / protein neddylation / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / positive regulation of intracellular estrogen receptor signaling pathway / androgen receptor signaling pathway / seminiferous tubule development / RUNX2 regulates osteoblast differentiation / nuclear steroid receptor activity / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / intracellular receptor signaling pathway / estrogen receptor signaling pathway / steroid binding / post-translational protein modification / insulin-like growth factor receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / NIK-->noncanonical NF-kB signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / SUMOylation of intracellular receptors / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / beta-catenin binding / protein modification process / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / transcription coactivator binding / multicellular organism growth / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / MAPK cascade / Neddylation / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / transcription cis-regulatory region binding / positive regulation of MAPK cascade / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / zinc ion binding / nucleoplasm
Similarity search - Function
E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Androgen receptor / Androgen receptor / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family ...E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Androgen receptor / Androgen receptor / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 5-ALPHA-DIHYDROTESTOSTERONE / TRIETHYLENE GLYCOL / Androgen receptor / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEstebanez-Perpina, E. / Fuentes-Prior, P.
CitationJournal: Nat Commun / Year: 2017
Title: Structure of the homodimeric androgen receptor ligand-binding domain.
Authors: Nadal, M. / Prekovic, S. / Gallastegui, N. / Helsen, C. / Abella, M. / Zielinska, K. / Gay, M. / Vilaseca, M. / Taules, M. / Houtsmuller, A.B. / van Royen, M.E. / Claessens, F. / Fuentes- ...Authors: Nadal, M. / Prekovic, S. / Gallastegui, N. / Helsen, C. / Abella, M. / Zielinska, K. / Gay, M. / Vilaseca, M. / Taules, M. / Houtsmuller, A.B. / van Royen, M.E. / Claessens, F. / Fuentes-Prior, P. / Estebanez-Perpina, E.
History
DepositionApr 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq.db_align_beg
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Androgen receptor
M: Unknown peptide
B: Androgen receptor
F: Unknown peptide
C: Androgen receptor
K: Unknown peptide
D: Androgen receptor
L: Unknown peptide
G: uba3-derived peptide
H: uba3-derived peptide
I: uba3-derived peptide
J: uba3-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,81740
Polymers122,91712
Non-polymers2,90028
Water1,78399
1
A: Androgen receptor
M: Unknown peptide
G: uba3-derived peptide
hetero molecules

A: Androgen receptor
M: Unknown peptide
G: uba3-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,72718
Polymers61,4446
Non-polymers1,28312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
2
B: Androgen receptor
F: Unknown peptide
C: Androgen receptor
K: Unknown peptide
H: uba3-derived peptide
I: uba3-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,99920
Polymers61,4736
Non-polymers1,52614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Androgen receptor
L: Unknown peptide
J: uba3-derived peptide
hetero molecules

D: Androgen receptor
L: Unknown peptide
J: uba3-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,90922
Polymers61,4446
Non-polymers1,46516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Unit cell
Length a, b, c (Å)91.090, 91.010, 157.230
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
15A
25B
35C
45D
16A
26B
36C
46D
17A
27B
37C
47D
18A
28D
19B
29C
110A
210B
310C
410D
111A
211B
311C
411D
112A
212B
312C
412D
113A
213B
313C
413D
114A
214B
314C
414D
115A
215B
315C
415D
116A
216B
316C
416D
117A
217B
317C
417D
118B
218D
119A
219B
319C
419D
120A
220B
320C
420D
121G
221H
321I
421J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A674 - 677
2115C674 - 677
1126A683 - 685
2126B683 - 685
3126C683 - 685
4126D683 - 685
1226A687 - 692
2226B687 - 692
3226C687 - 692
4226D687 - 692
1135A697 - 711
2135B697 - 711
3135C697 - 711
4135D697 - 711
1235A713 - 716
2235B713 - 716
3235C713 - 716
4235D713 - 716
1335A718 - 719
2335B718 - 719
3335C718 - 719
4335D718 - 719
1146A723 - 725
2146B723 - 725
1155A732 - 734
2155B732 - 734
3155C732 - 734
4155D732 - 734
1255A737 - 747
2255B737 - 747
3255C737 - 747
4255D737 - 747
1355A750 - 751
2355B750 - 751
3355C750 - 751
4355D750 - 751
1455A753 - 755
2455B753 - 755
3455C753 - 755
4455D753 - 755
1166A758 - 760
2166B758 - 760
3166C758 - 760
4166D758 - 760
1266A765 - 770
2266B765 - 770
3266C765 - 770
4266D765 - 770
1175A762 - 766
2175B762 - 766
3175C762 - 766
4175D762 - 766
1186A773 - 779
2186D773 - 779
1196B773 - 779
2196C773 - 779
11105A782 - 785
21105B782 - 785
31105C782 - 785
41105D782 - 785
12105A790 - 796
22105B790 - 796
32105C790 - 796
42105D790 - 796
11116A797 - 798
21116B797 - 798
31116C797 - 798
41116D797 - 798
12116A800 - 802
22116B800 - 802
32116C800 - 802
42116D800 - 802
11125A803 - 805
21125B803 - 805
31125C803 - 805
41125D803 - 805
12125A807 - 809
22125B807 - 809
32125C807 - 809
42125D807 - 809
11136A816 - 821
21136B816 - 821
31136C816 - 821
41136D816 - 821
11145A830 - 833
21145B830 - 833
31145C830 - 833
41145D830 - 833
12145A835 - 840
22145B835 - 840
32145C835 - 840
42145D835 - 840
11155A858 - 863
21155B858 - 863
31155C858 - 863
41155D858 - 863
12155A865 - 870
22155B865 - 870
32155C865 - 870
42155D865 - 870
13155A872 - 874
23155B872 - 874
33155C872 - 874
43155D872 - 874
14155A876 - 879
24155B876 - 879
34155C876 - 879
44155D876 - 879
11165A894 - 896
21165B894 - 896
31165C894 - 896
41165D894 - 896
12165A898 - 901
22165B898 - 901
32165C898 - 901
42165D898 - 901
13165A903 - 908
23165B903 - 908
33165C903 - 908
43165D903 - 908
11176A913 - 917
21176B913 - 917
31176C913 - 917
41176D913 - 917
11185B674 - 677
21185D674 - 677
11196A884 - 885
21196B884 - 885
31196C884 - 885
41196D884 - 885
12196A887 - 889
22196B887 - 889
32196C887 - 889
42196D887 - 889
11206A503 - 505
21206B503 - 505
31206C503 - 505
41206D503 - 505
11215G63 - 67
21215H63 - 67
31215I63 - 67
41215J63 - 67

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.000316, -0.999844, -0.017666), (0.999944, 0.000128, 0.01062), (-0.010616, -0.017668, 0.999788)-43.79139, 46.51652, -39.83731
3given(1), (1), (1)
4given(0.023297, 0.999728, -0.001195), (0.999719, -0.023302, -0.004276), (-0.004302, -0.001095, -0.99999)-45.26199, 47.13073, 38.98962
5given(0.013674, -0.99982, -0.013178), (0.999906, 0.013685, -0.00072), (0.000901, -0.013167, 0.999913)-43.09274, 46.93977, -39.36037
6given(0.999937, -0.008852, 0.006883), (-0.008849, -0.999961, -0.000436), (0.006887, 0.000375, -0.999976)-0.27232, 2.10419, 78.87052
7given(1), (1), (1)
8given(0.003221, 0.999988, 0.003812), (0.999995, -0.003223, 0.000532), (0.000545, 0.00381, -0.999993)-46.63187, 46.83416, 39.3051
9given(-0.001677, -0.999949, -0.009918), (0.999997, -0.00166, -0.001666), (0.001649, -0.009921, 0.999949)-44.09138, 46.81554, -39.35427
10given(0.999976, -0.006934, 0.000822), (-0.006932, -0.999974, -0.001731), (0.000834, 0.001726, -0.999998)0.15322, 2.28914, 78.68183
11given(1), (1), (1)
12given(-0.000152, 0.999991, 0.004258), (0.999973, 0.00012, 0.007376), (0.007376, 0.004259, -0.999964)-46.78967, 46.35187, 39.63618
13given(1), (1), (1)
14given(0.005624, 0.999976, 0.004053), (0.999954, -0.005655, 0.007687), (0.007709, 0.004009, -0.999962)-46.53039, 46.54606, 39.62396
15given(0.002944, -0.999991, -0.003024), (0.999995, 0.002947, -0.000886), (0.000895, -0.003022, 0.999995)-44.05925, 46.82366, -39.31577
16given(0.999987, -0.003277, 0.003952), (-0.003284, -0.999993, 0.001861), (0.003946, -0.001874, -0.99999)-0.18579, 2.08938, 78.77569
17given(1), (1), (1)
18given(-0.005485, 0.999984, -0.001147), (0.999976, 0.00549, 0.004239), (0.004245, -0.001124, -0.99999)-46.97253, 46.62865, 39.52848
19given(0.002707, -0.998879, -0.047261), (0.999993, 0.002826, -0.002447), (0.002578, -0.047255, 0.99888)-42.06106, 46.85879, -39.51848
20given(0.999916, -0.011884, 0.005199), (-0.011873, -0.999927, -0.002068), (0.005223, 0.002007, -0.999984)-0.14964, 2.10539, 78.83051
21given(1), (1), (1)
22given(0.014842, 0.999867, 0.006799), (0.999863, -0.014792, -0.00743), (-0.007328, 0.006908, -0.999949)-46.10224, 47.18075, 38.84374
23given(0.017597, -0.99982, -0.007112), (0.999747, 0.017495, 0.014156), (-0.014029, -0.007359, 0.999874)-43.08873, 46.316, -40.1293
24given(0.999932, -0.011151, 0.003395), (-0.011107, -0.999854, -0.012968), (0.003539, 0.012929, -0.99991)-0.02585, 2.91209, 78.60371
25given(1), (1), (1)
26given(0.999971, -0.006013, -0.004734), (-0.00599, -0.99997, 0.00489), (-0.004763, -0.004861, -0.999977)0.46484, 1.87105, 78.59437
27given(1), (1), (1)
28given(0.999927, 0.011995, 0.001442), (0.011992, -0.999926, 0.002007), (0.001466, -0.00199, -0.999997)0.09024, 2.90163, 78.67081
29given(1), (1), (1)
30given(0.003154, 0.999993, 0.001886), (0.999983, -0.003164, 0.004867), (0.004873, 0.001871, -0.999986)-46.58306, 46.6615, 39.50385
31given(0.003971, -0.999987, -0.00308), (0.99999, 0.003977, -0.001857), (0.001869, -0.003073, 0.999994)-43.99455, 46.89056, -39.27118
32given(0.999976, -0.001818, 0.006756), (-0.001809, -0.999997, -0.001341), (0.006758, 0.001329, -0.999976)-0.32634, 2.4003, 78.86474
33given(1), (1), (1)
34given(0.008809, 0.999961, 0.001148), (0.999933, -0.008818, 0.007531), (0.00754, 0.001081, -0.999971)-46.40404, 46.54506, 39.59737
35given(0.040648, -0.999165, -0.004247), (0.999084, 0.040587, 0.013573), (-0.01339, -0.004795, 0.999899)-42.72921, 46.32561, -39.81874
36given(0.999966, -0.007427, 0.003531), (-0.007443, -0.999963, 0.004393), (0.003498, -0.00442, -0.999984)-0.18286, 1.71025, 78.731
37given(1), (1), (1)
38given(-0.012346, 0.999895, 0.007583), (0.999892, 0.012406, -0.007902), (-0.007995, 0.007485, -0.99994)-47.44468, 46.97636, 38.95842
39given(-0.008438, -0.999952, -0.005048), (0.999938, -0.008474, 0.007236), (-0.007278, -0.004987, 0.999961)-44.46091, 46.46205, -39.61318
40given(0.999889, 0.011161, 0.009846), (0.011156, -0.999938, 0.000473), (0.00985, -0.000363, -0.999951)-0.61226, 2.72742, 78.98257
41given(1), (1), (1)
42given(-0.012171, 0.999923, 0.002604), (0.999872, 0.012198, -0.010386), (-0.010417, 0.002477, -0.999943)-47.21254, 46.8151, 38.8833
43given(0.017946, -0.999811, -0.007443), (0.999837, 0.01793, 0.002139), (-0.002005, -0.00748, 0.99997)-43.24786, 47.17422, -39.51352
44given(0.999927, 0.0109, 0.005237), (0.010915, -0.999936, -0.002848), (0.005205, 0.002905, -0.999982)-0.2064, 2.7124, 78.81425
45given(1), (1), (1)
46given(0.00901, 0.999901, 0.010829), (0.999912, -0.009114, 0.009647), (0.009745, 0.010741, -0.999895)-46.88901, 46.44173, 39.45358
47given(-0.000483, -0.999994, -0.003448), (0.999995, -0.000493, 0.002972), (-0.002974, -0.003446, 0.99999)-44.1328, 46.63429, -39.45292
48given(0.999928, -0.010338, 0.006088), (-0.010375, -0.999928, 0.006036), (0.006025, -0.006099, -0.999963)-0.517, 1.47794, 78.74889
49given(1), (1), (1)
50given(0.002797, 0.999984, -0.004933), (0.999993, -0.002809, -0.002408), (-0.002422, -0.004927, -0.999985)-46.34921, 46.89388, 39.3509
51given(0.00389, -0.999991, -0.001549), (0.999991, 0.003893, -0.00164), (0.001646, -0.001543, 0.999997)-44.07048, 46.84052, -39.27906
52given(0.999998, -0.002159, -0.000154), (-0.002159, -0.999994, -0.002755), (-0.000148, 0.002755, -0.999996)0.13812, 2.46112, 78.65284
53given(1), (1), (1)
54given(0.004005, 0.999982, 0.004402), (0.999977, -0.004029, 0.005413), (0.00543, 0.004381, -0.999976)-46.59394, 46.62746, 39.53364
55given(0.010487, -0.99994, -0.00305), (0.999945, 0.01049, -0.000711), (0.000743, -0.003042, 0.999995)-43.63243, 46.98188, -39.34861
56given(0.999971, -0.007166, 0.002702), (-0.007165, -0.999974, -0.000556), (0.002706, 0.000537, -0.999996)0.00762, 2.24662, 78.74776
57given(1), (1), (1)
58given(-0.004457, 0.999811, -0.018931), (0.999783, 0.00407, -0.020421), (-0.02034, -0.019018, -0.999612)-45.98535, 47.46567, 39.11417
59given(-0.00438, -0.999969, 0.006488), (0.999807, -0.004255, 0.019159), (-0.01913, 0.006571, 0.999795)-44.69244, 45.80342, -39.87354
60given(0.999724, 0.000918, -0.02348), (0.000833, -0.999993, -0.003636), (-0.023484, 0.003615, -0.999718)2.07947, 2.61327, 78.14843
61given(1), (1), (1)
62given(0.009115, -0.99982, -0.016613), (0.999958, 0.009115, 5.5E-5), (9.6E-5, -0.016613, 0.999862)-42.53052, 46.83261, -39.35431
63given(1), (1), (1)
64given(0.024246, 0.999706, -0.000399), (0.999475, -0.024232, 0.021517), (0.021501, -0.00092, -0.999768)-45.07022, 46.58771, 40.77804
65given(-0.007708, -0.99996, -0.004562), (0.99997, -0.007708, -1.1E-5), (-2.4E-5, -0.004562, 0.99999)-44.73648, 46.54437, -39.40161
66given(0.999959, -0.007787, -0.004688), (-0.007787, -0.99997, -0.000125), (-0.004687, 0.000161, -0.999989)0.67203, 2.18758, 78.61052
67given(1), (1), (1)
68given(-0.057914, 0.997385, 0.043239), (0.973475, 0.066022, -0.21906), (-0.221342, 0.029405, -0.974753)-49.99461, 55.9025, 33.15948
69given(-0.119143, -0.992234, 0.035721), (0.986247, -0.11412, 0.119555), (-0.11455, 0.049474, 0.992185)-47.99316, 41.82531, -41.03312
70given(0.996718, -0.057874, 0.056604), (-0.046713, -0.98224, -0.181719), (0.066116, 0.178478, -0.98172)-6.44726, 16.74751, 83.61742
71given(1), (1), (1)
72given(-0.028577, 0.999362, 0.021438), (0.998572, 0.027572, 0.045768), (0.045147, 0.022715, -0.998722)-49.23615, 43.60556, 41.34041
73given(-0.034795, -0.997027, -0.068743), (0.998759, -0.032238, -0.037965), (0.035636, -0.069979, 0.996912)-44.62617, 47.03252, -38.67539
74given(0.999988, -0.003631, -0.003338), (-0.003615, -0.999982, 0.004775), (-0.003355, -0.004762, -0.999983)0.5158, 2.06379, 78.66383

-
Components

-
Protein , 2 types, 4 molecules ACDB

#1: Protein Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 29406.455 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#3: Protein Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 29435.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275

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Protein/peptide , 2 types, 8 molecules MFKLGHIJ

#2: Protein/peptide
Unknown peptide


Mass: 379.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide
uba3-derived peptide


Mass: 936.061 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4*PLUS

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Non-polymers , 9 types, 127 molecules

#5: Chemical
ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H30O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-SO4 / SULFATE ION / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli)
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES 1.35 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2015 / Details: Channel-cut Si(111) + KB focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→78.61 Å / Num. obs: 69531 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.073 / Net I/av σ(I): 6.8 / Net I/σ(I): 8.9
Reflection shellResolution: 2.15→2.27 Å / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T7T

1t7t


Resolution: 2.15→157.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.643 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24312 3444 4.9 %RANDOM
Rwork0.20116 ---
obs0.2032 66522 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.16 Å2
2---0.18 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.15→157.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8546 0 174 99 8819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0198937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4881.97712052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51323.711415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.106151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5841556
X-RAY DIFFRACTIONr_chiral_restr0.1730.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216570
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_it2.0282.4594172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9723.6595191
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3942.8244765
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.38911.24213224
X-RAY DIFFRACTIONr_long_range_B_other
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A16medium positional0.050.5
31A84medium positional0.080.5
32B84medium positional0.070.5
33C84medium positional0.070.5
34D84medium positional0.070.5
51A76medium positional0.070.5
52B76medium positional0.080.5
53C76medium positional0.080.5
54D76medium positional0.060.5
71A20medium positional0.060.5
72B20medium positional0.060.5
73C20medium positional0.060.5
74D20medium positional0.050.5
101A44medium positional0.060.5
102B44medium positional0.060.5
103C44medium positional0.060.5
104D44medium positional0.070.5
121A24medium positional0.060.5
122B24medium positional0.070.5
123C24medium positional0.060.5
124D24medium positional0.060.5
141A40medium positional0.060.5
142B40medium positional0.070.5
143C40medium positional0.060.5
144D40medium positional0.060.5
151A76medium positional0.070.5
152B76medium positional0.070.5
153C76medium positional0.060.5
154D76medium positional0.070.5
161A52medium positional0.080.5
162B52medium positional0.070.5
163C52medium positional0.090.5
164D52medium positional0.080.5
181A16medium positional0.060.5
211A20medium positional0.160.5
212B20medium positional0.130.5
213C20medium positional0.150.5
214D20medium positional0.190.5
11A15loose positional0.515
21A61loose positional0.215
22B61loose positional0.175
23C61loose positional0.195
24D61loose positional0.235
31A81loose positional0.125
32B81loose positional0.125
33C81loose positional0.145
34D81loose positional0.15
41A22loose positional0.045
51A86loose positional0.125
52B86loose positional0.115
53C86loose positional0.115
54D86loose positional0.115
61A71loose positional0.355
62B71loose positional0.355
63C71loose positional0.855
64D71loose positional0.445
71A23loose positional0.095
72B23loose positional0.085
73C23loose positional0.115
74D23loose positional0.075
81A67loose positional0.085
91A67loose positional0.235
101A45loose positional0.115
102B45loose positional0.125
103C45loose positional0.125
104D45loose positional0.145
111A40loose positional0.265
112B40loose positional0.265
113C40loose positional0.275
114D40loose positional0.265
121A26loose positional0.225
122B26loose positional0.555
123C26loose positional0.25
124D26loose positional0.25
131A40loose positional0.275
132B40loose positional0.295
133C40loose positional0.365
134D40loose positional0.35
141A47loose positional0.445
142B47loose positional0.225
143C47loose positional0.215
144D47loose positional0.25
151A79loose positional0.345
152B79loose positional0.45
153C79loose positional0.455
154D79loose positional0.435
161A43loose positional0.145
162B43loose positional0.175
163C43loose positional0.165
164D43loose positional0.155
171A48loose positional0.115
172B48loose positional0.15
173C48loose positional0.135
174D48loose positional0.115
181A15loose positional0.485
191A36loose positional0.065
192B36loose positional0.095
193C36loose positional0.15
194D36loose positional0.075
201A24loose positional0.635
202B24loose positional0.325
203C24loose positional0.415
204D24loose positional0.395
211A24loose positional1.065
212B24loose positional0.615
213C24loose positional1.065
214D24loose positional0.875
11A16medium thermal1.452
31A84medium thermal1.632
32B84medium thermal1.112
33C84medium thermal1.222
34D84medium thermal1.252
51A76medium thermal1.592
52B76medium thermal1.32
53C76medium thermal1.062
54D76medium thermal1.362
71A20medium thermal0.922
72B20medium thermal1.182
73C20medium thermal0.772
74D20medium thermal1.312
101A44medium thermal1.092
102B44medium thermal1.272
103C44medium thermal1.072
104D44medium thermal1.422
121A24medium thermal1.232
122B24medium thermal0.842
123C24medium thermal1.52
124D24medium thermal0.962
141A40medium thermal1.472
142B40medium thermal1.32
143C40medium thermal1.472
144D40medium thermal1.12
151A76medium thermal1.082
152B76medium thermal2.082
153C76medium thermal1.32
154D76medium thermal1.622
161A52medium thermal1.472
162B52medium thermal1.482
163C52medium thermal1.42
164D52medium thermal1.392
181A16medium thermal1.392
211A20medium thermal6.232
212B20medium thermal3.822
213C20medium thermal3.482
214D20medium thermal6.242
11A15loose thermal2.8310
21A61loose thermal1.8910
22B61loose thermal2.810
23C61loose thermal2.2510
24D61loose thermal2.910
31A81loose thermal1.8910
32B81loose thermal2.2310
33C81loose thermal1.8910
34D81loose thermal1.910
41A22loose thermal0.6510
51A86loose thermal2.0810
52B86loose thermal2.4310
53C86loose thermal2.0410
54D86loose thermal1.6110
61A71loose thermal1.7610
62B71loose thermal1.4710
63C71loose thermal2.1110
64D71loose thermal2.2910
71A23loose thermal1.2610
72B23loose thermal1.3810
73C23loose thermal1.3810
74D23loose thermal1.3910
81A67loose thermal1.210
91A67loose thermal1.3510
101A45loose thermal1.6810
102B45loose thermal2.3610
103C45loose thermal1.6710
104D45loose thermal1.7510
111A40loose thermal1.4410
112B40loose thermal1.6710
113C40loose thermal1.5110
114D40loose thermal1.5610
121A26loose thermal1.1910
122B26loose thermal1.4710
123C26loose thermal1.410
124D26loose thermal0.7710
131A40loose thermal2.4310
132B40loose thermal2.2110
133C40loose thermal3.4910
134D40loose thermal1.9510
141A47loose thermal1.7810
142B47loose thermal1.9910
143C47loose thermal2.7410
144D47loose thermal2.4610
151A79loose thermal2.2310
152B79loose thermal2.0110
153C79loose thermal1.910
154D79loose thermal2.4910
161A43loose thermal1.8810
162B43loose thermal2.1610
163C43loose thermal2.1810
164D43loose thermal1.8610
171A48loose thermal2.4810
172B48loose thermal2.0810
173C48loose thermal2.5210
174D48loose thermal2.8910
181A15loose thermal0.9310
191A36loose thermal1.7510
192B36loose thermal2.1310
193C36loose thermal2.4410
194D36loose thermal2.3910
201A24loose thermal7.2310
202B24loose thermal9.6210
203C24loose thermal2.9510
204D24loose thermal3.2610
211A24loose thermal5.9210
212B24loose thermal6.6210
213C24loose thermal5.2810
214D24loose thermal6.0710
LS refinement shellResolution: 2.147→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 254 -
Rwork0.233 4706 -
obs--96.91 %
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)
15.77237.7405-1.014813.02454.251112.1114-0.1499-0.0023-0.0947-0.5118-0.0013-0.0868-0.5875-0.0830.15120.1692-0.02650.01950.2514-0.03140.1666-38.15827.515-9.096
213.40480.1114-7.39540.2827-1.775422.3556-0.7139-0.3480.031-0.13880.04740.01810.7302-0.05110.66650.19050.00120.02380.22030.05050.1931-18.9938.6147.936
320.8903-12.877923.425712.4259-9.91630.83250.01350.71130.79690.396-0.1485-1.23290.41941.08410.1350.09020.02060.00820.2410.04740.2866-18.949-6.47730.403
49.8035-10.3082-2.79110.90622.2717.41930.1780.1585-0.1691-0.2066-0.17930.19290.30590.11860.00130.1228-0.0620.06890.1648-0.03640.1622-38.305-25.25387.285
54.3798-6.01781.251812.0768-2.34380.4618-0.17120.1379-0.1742-0.42040.1464-0.19520.0747-0.02920.02490.3129-0.07440.17570.3137-0.030.1039-24.413-10.298-18.299
610.5817-5.69163.97293.0798-2.18471.6865-0.0354-0.0216-0.09410.0325-0.03970.0374-0.0482-0.02330.07510.195-0.03210.06220.3151-0.10980.1369-57.24421.45958.123
78.52462.407-3.18722.8890.26741.8090.20740.4259-0.3151-0.2437-0.3317-0.0481-0.2503-0.3870.12430.17440.01410.08710.2642-0.04980.0955-57.367-19.45720.74
88.22279.48691.433810.96721.263812.24670.1519-0.14610.10990.2332-0.14930.1244-0.58640.237-0.00260.18770.0536-0.04140.21260.05090.0456-25.04112.77297.226
90.0457-0.021-0.00310.0333-0.00870.0082-0.0251-0-0.02130.03630.0230.0392-0.00020.01450.00210.15-0.00880.14310.25690.0370.1452-43.9040.23948.039
100.2532-0.0990.14590.4401-0.29520.3362-0.0389-0.02740.0245-0.0272-0.0074-0.00420.04330.03720.04620.08660.00150.04210.21760.01620.1402-29.260.51-1.706
110.5405-0.11980.42280.2771-0.10490.3814-0.0413-0.0291-0.0022-0.0375-0.0302-0.0211-0.0597-0.02250.07140.144-0.0020.02080.16580.00340.1335-46.37917.42340.952
120.27730.1218-0.26750.4121-0.12260.2936-0.00950.00870.0160.0318-0.0231-0.03420.0601-0.02540.03270.1324-0.00330.05770.1764-0.00470.1351-46.327-14.9837.575
130.32560.12230.04610.66-0.32880.2502-0.03870.0547-0.03530.0463-0.0293-0.0073-0.04110.04580.0680.0848-0.00940.03950.21250.0140.1395-29.4372.04280.36
141.2527-1.8695-2.84662.79654.25416.474-0.03840.0211-0.00970.09420.00530.01670.131-0.02470.03310.1550.02280.01380.20520.03160.1698-28.414-8.5052.001
150.4460.64160.5030.92380.72490.56960.0267-0.0081-0.01410.0262-0.017-0.01610.0118-0.0236-0.00970.17990.03120.00230.18180.01030.1676-55.36318.23837.268
160.7933-0.46571.22893.97871.85093.68990.008-0.08190.0453-0.0954-0.0052-0.1343-0.0489-0.1694-0.00280.1505-0.01330.04520.17260.00350.175-55.346-15.92441.322
171.2269-0.51060.97310.2141-0.4030.7742-0.0718-0.04020.03840.02020.0287-0.0059-0.0703-0.0180.04310.1619-0.03390.01410.17740.02340.1894-28.52510.91976.554
180.0032-0.00260.00640.00860.01670.1670.0014-0.0071-0.00160.01-0.01060.0120.01370.04160.00920.0894-0.00920.10440.27560.02730.1298-39.534-0.05237.303
190.01510.0599-0.0240.2662-0.08811.3485-0.0090.01750.00290.0146-0.01210.02870.0558-0.06020.02110.0487-0.02980.06620.2347-0.0020.0982-51.899-3.73742.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1002
2X-RAY DIFFRACTION1M503 - 505
3X-RAY DIFFRACTION2B1002
4X-RAY DIFFRACTION2F503 - 505
5X-RAY DIFFRACTION3C1002
6X-RAY DIFFRACTION3K503 - 505
7X-RAY DIFFRACTION4D1002
8X-RAY DIFFRACTION4L503 - 505
9X-RAY DIFFRACTION5G62 - 68
10X-RAY DIFFRACTION6H62 - 69
11X-RAY DIFFRACTION7I62 - 69
12X-RAY DIFFRACTION8J62 - 69
13X-RAY DIFFRACTION9S1601 - 3001
14X-RAY DIFFRACTION10A668 - 919
15X-RAY DIFFRACTION11B669 - 919
16X-RAY DIFFRACTION12C668 - 917
17X-RAY DIFFRACTION13D669 - 917
18X-RAY DIFFRACTION14A1001
19X-RAY DIFFRACTION15B1001
20X-RAY DIFFRACTION16C1001
21X-RAY DIFFRACTION17D1001
22X-RAY DIFFRACTION18S4001 - 4099
23X-RAY DIFFRACTION19S6001 - 6005

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