- PDB-3q6m: Crystal Structure of Human MC-HSP90 in C2221 Space Group -
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Basic information
Entry
Database: PDB / ID: 3q6m
Title
Crystal Structure of Human MC-HSP90 in C2221 Space Group
Components
Heat shock protein HSP 90-alpha
Keywords
CHAPERONE / three domains / trimer of dimer / hexamer
Function / homology
Function and homology information
sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / positive regulation of protein import into nucleus / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding Similarity search - Function
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 35.924 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.985 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25163
2185
5 %
RANDOM
Rwork
0.2086
-
-
-
obs
0.21094
41365
99.18 %
-
all
-
41749
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 104.496 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.51 Å2
0 Å2
0 Å2
2-
-
-2.4 Å2
0 Å2
3-
-
-
2.91 Å2
Refinement step
Cycle: LAST / Resolution: 3→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9197
0
15
133
9345
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
9373
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.405
1.982
12592
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.332
5
1103
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.161
24.923
455
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.599
15
1895
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.224
15
54
X-RAY DIFFRACTION
r_chiral_restr
0.104
0.2
1392
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
6882
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.564
1.5
5568
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.109
2
9051
X-RAY DIFFRACTION
r_scbond_it
1.478
3
3805
X-RAY DIFFRACTION
r_scangle_it
2.645
4.5
3541
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.003→3.08 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.333
139
-
Rwork
0.261
2909
-
obs
-
-
95.28 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
10.326
0.5494
-2.4375
10
0.549
5.6767
0.1648
0.921
0.2407
-0.4142
-0.1621
-0.2853
-0.321
-0.0257
-0.0027
0.031
0.0102
0.0542
0.356
0.0017
0.3251
-15.084
-39.835
-4.187
2
23.1677
5.4715
-8.3829
7.1841
1.6042
6.7108
0.6541
-2.1393
0.7811
0.9372
-0.7653
0.2337
-0.2249
0.7248
0.1111
0.2883
-0.1618
-0.0431
0.4277
-0.0171
0.5445
-12.269
-35.972
7.668
3
5.1593
3.1607
-2.0566
4.4504
-2.126
1.0889
0.4054
-0.0572
0.5293
0.5099
0.005
0.222
-0.2846
0.0747
-0.4104
0.2281
-0.0792
0.1138
0.4714
-0.1653
0.5403
-44.844
-51.811
12.989
4
5.9518
-1.51
-2.2194
5.1924
0.6801
5.2518
-0.0836
-0.2864
-0.0581
0.5755
0.1612
0.236
0.3617
0.2685
-0.0776
0.2712
-0.0336
-0.0972
0.3608
0.0094
0.2198
-56.027
-75.001
27.422
5
9.3786
-0.4757
-0.0573
6.9247
1.1757
7.3289
-0.2826
-0.1924
0.637
0.1678
-0.0436
-0.1147
-0.0403
0.1279
0.3263
0.156
-0.0344
-0.0128
0.1937
0.0863
0.3466
2.213
-65.745
48.035
6
21.306
13.7397
-0.1118
13.4306
2.746
5.3572
-0.8268
1.5437
-0.0262
-0.8776
0.482
-0.3054
-0.3065
0.2146
0.3448
0.2061
-0.0246
0.019
0.4213
0.2258
0.3107
6.491
-64.702
36.124
7
6.4103
2.1745
3.3526
2.1153
1.3268
2.7927
0.086
0.5818
-0.4817
-0.0896
0.1611
-0.1047
0.0642
0.2588
-0.2471
0.1552
-0.0036
0.1
0.409
-0.0988
0.4213
-21.766
-87.204
31.042
8
8.357
-3.9793
1.9553
6.9404
0.3621
4.3083
0.4697
1.0533
-0.4549
-0.6739
-0.1939
0.4453
0.025
-0.5865
-0.2759
0.1976
-0.0023
-0.0638
0.6694
-0.0754
0.2374
-48.189
-87.361
17.041
9
10.7687
2.8608
1.0463
13.5197
-0.9458
5.7409
-0.2391
-0.7859
-0.4874
0.6558
0.3175
-0.0668
0.2421
0.0432
-0.0785
0.1026
0.101
0.0713
0.2397
0.054
0.4063
-13.605
-41.841
48.786
10
3.6085
-1.144
1.6856
25.5556
-3.8337
6.3676
-0.1779
0.5778
-0.7514
-2.0859
0.2151
-0.0195
0.4408
0.2462
-0.0372
0.3036
0.0556
0.0279
0.2439
-0.064
0.4858
-15.878
-46.736
37.222
11
1.2313
-0.0055
0.2304
12.9539
-1.6646
1.5243
-0.1359
0.1345
0.0888
-1.8138
0.3197
0.9352
-0.154
-0.0801
-0.1838
0.5624
-0.0284
-0.0913
0.1903
0.0912
0.4477
-20.175
-10.438
31.296
12
12.7823
2.6852
-0.5669
3.4851
-0.4665
0.5569
-0.7187
0.6395
0.8918
-1.459
0.7046
0.1953
0.4844
-0.0988
0.0141
1.9844
-0.0139
0.2658
0.429
0.1801
0.3202
-7.287
11.483
16.586
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
294 - 349
2
X-RAY DIFFRACTION
2
A
359 - 395
3
X-RAY DIFFRACTION
3
A
405 - 615
4
X-RAY DIFFRACTION
4
A
630 - 697
5
X-RAY DIFFRACTION
5
B
294 - 349
6
X-RAY DIFFRACTION
6
B
359 - 395
7
X-RAY DIFFRACTION
7
B
405 - 615
8
X-RAY DIFFRACTION
8
B
630 - 699
9
X-RAY DIFFRACTION
9
C
294 - 349
10
X-RAY DIFFRACTION
10
C
360 - 395
11
X-RAY DIFFRACTION
11
C
406 - 614
12
X-RAY DIFFRACTION
12
C
630 - 697
+
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