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- PDB-8smo: Crystal structure of the complex between truncated MLLE domain of... -

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Basic information

Entry
Database: PDB / ID: 8smo
TitleCrystal structure of the complex between truncated MLLE domain of PABPC1 and engineered superPAM2 peptide
Components
  • Polyadenylate-binding protein 1
  • superPAM2
KeywordsPEPTIDE BINDING PROTEIN / MLLE domain / poly(A) binding protein / PAM2 motif / complex
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / : / cell leading edge / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structure of the complex between truncated MLLE domain of PABPC1 and engineered superPAM2 peptide
Authors: Behvarmanesh, A. / Kozlov, G. / Chen, Y.S. / Gehring, K.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1
B: superPAM2
C: Polyadenylate-binding protein 1
D: superPAM2
E: Polyadenylate-binding protein 1
F: superPAM2
G: Polyadenylate-binding protein 1
H: superPAM2
I: Polyadenylate-binding protein 1
J: superPAM2
K: Polyadenylate-binding protein 1
L: superPAM2
M: Polyadenylate-binding protein 1
N: superPAM2
O: Polyadenylate-binding protein 1
P: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,30622
Polymers85,73016
Non-polymers5766
Water32418
1
A: Polyadenylate-binding protein 1
B: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Polyadenylate-binding protein 1
D: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Polyadenylate-binding protein 1
F: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Polyadenylate-binding protein 1
H: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Polyadenylate-binding protein 1
J: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Polyadenylate-binding protein 1
L: superPAM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8123
Polymers10,7162
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Polyadenylate-binding protein 1
N: superPAM2


Theoretical massNumber of molelcules
Total (without water)10,7162
Polymers10,7162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Polyadenylate-binding protein 1
P: superPAM2


Theoretical massNumber of molelcules
Total (without water)10,7162
Polymers10,7162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.275, 108.275, 75.866
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 554 or (resid 555 through 559...
d_2ens_1(chain "C" and (resid 554 or (resid 555 through 559...
d_3ens_1(chain "E" and (resid 554 or (resid 555 through 559...
d_4ens_1(chain "G" and (resid 554 or (resid 555 through 559...
d_5ens_1(chain "I" and (resid 554 or (resid 555 through 559...
d_6ens_1(chain "K" and (resid 554 or (resid 555 through 559...
d_7ens_1(chain "M" and ((resid 554 through 559 and (name N...
d_1ens_2(chain "B" and ((resid 1 and (name N or name...
d_2ens_2(chain "D" and ((resid 1 and (name N or name...
d_3ens_2(chain "F" and ((resid 1 and (name N or name...
d_4ens_2(chain "H" and (resid 1 through 5 or (resid 6...
d_5ens_2(chain "J" and ((resid 1 and (name N or name...
d_1ens_3(chain "L" and (resid 3 or (resid 4 and (name...
d_2ens_3chain "N"
d_3ens_3chain "P"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYGLUGLUAA554 - 5984 - 48
d_12ens_1LEULEUGLUGLUAA603 - 62153 - 71
d_21ens_1GLYGLYGLUGLUCC554 - 5984 - 48
d_22ens_1LEULEUGLUGLUCC603 - 62153 - 71
d_31ens_1GLYGLYGLUGLUEE554 - 5984 - 48
d_32ens_1LEULEUGLUGLUEE603 - 62153 - 71
d_41ens_1GLYGLYGLUGLUGG554 - 5984 - 48
d_42ens_1LEULEUGLUGLUGG603 - 62153 - 71
d_51ens_1GLYGLYGLUGLUII554 - 5984 - 48
d_52ens_1LEULEUGLUGLUII603 - 62153 - 71
d_61ens_1GLYGLYGLUGLUKK554 - 5984 - 48
d_62ens_1LEULEUGLUGLUKK603 - 62153 - 71
d_71ens_1GLYGLYGLUGLUMM554 - 6214 - 71
d_11ens_2SERSERGLYGLYBB1 - 181 - 18
d_21ens_2SERSERGLYGLYDD1 - 181 - 18
d_31ens_2SERSERGLYGLYFF1 - 181 - 18
d_41ens_2SERSERGLYGLYHH1 - 181 - 18
d_51ens_2SERSERGLYGLYJJ1 - 181 - 18
d_11ens_3LEULEUGLYGLYLL3 - 183 - 18
d_21ens_3LEULEUGLYGLYNN3 - 183 - 18
d_31ens_3LEULEUGLYGLYPP3 - 183 - 18

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.498001172535, 0.867172707992, -0.00251528660994), (0.867172047582, 0.497987460427, -0.00459664546639), (-0.00273350430564, -0.00447032107178, -0.999986271998)53.9514566576, -31.5546438443, -93.9805534725
2given(-0.0909318452883, 0.318396603355, -0.943586245387), (0.522176139561, -0.791565482536, -0.317421117966), (-0.847976107438, -0.52158191095, -0.0942805991959)2.02682203397, -64.8260764839, 1.07611454078
3given(0.496936003001, -0.845350596609, 0.196053507327), (0.184906842864, -0.117586450093, -0.975696103414), (0.847858519084, 0.521110156846, 0.0978781694158)-3.05283268657, -61.9611633054, -94.9350541989
4given(-0.0566368956969, 0.866495272368, 0.495961898748), (0.995407562175, 0.0106081804817, 0.0951380663679), (0.0771754313961, 0.499072549306, -0.863116761115)52.571525047, -70.9251469165, -62.3647751075
5given(0.88902946222, -0.4226133113, -0.176138026607), (0.452587700255, 0.753017726781, 0.477628178326), (-0.0692169696175, -0.504343426908, 0.860724531341)-33.8271165718, -21.4576603641, -32.2509358388
6given(-0.00745615693577, 0.158020542762, 0.987407673552), (-0.153977590855, -0.97584007817, 0.155006591319), (0.988046207036, -0.150882901295, 0.0316076392472)84.458469501, -17.6903178251, -73.1207037523
7given(-0.491109941633, 0.869986182752, 0.0439893970139), (0.871097255342, 0.490438360987, 0.0256862961248), (0.000772634942401, 0.0509338383936, -0.998701730819)55.1188036651, -30.867832025, -92.8250931204
8given(-0.0967353590781, 0.339926434204, -0.935463676277), (0.553804774512, -0.762561251203, -0.334365981959), (-0.827008187403, -0.550409263633, -0.114486245791)3.0620746137, -65.6761379829, -1.79093810943
9given(0.517166363258, -0.834425237104, 0.19045596971), (0.183460232847, -0.109277053898, -0.976934423825), (0.835991205503, 0.540178719661, 0.0965694317407)-3.45564664936, -61.5965571194, -93.5609011936
10given(-0.0567530419343, 0.86611823028, 0.496606789531), (0.997062031447, 0.0235392289967, 0.0728917700766), (0.0514431499607, 0.499284604084, -0.864909525007)52.4616692854, -71.1729847551, -61.0259444224
11given(-0.228438462777, 0.505326596114, 0.8321423556), (0.270684915403, -0.788073889847, 0.552873602838), (0.935171398887, 0.351545979071, 0.0432421010316)113.635413831, -11.2782369501, -32.560184215
12given(0.361411349993, -0.929138785311, 0.0779932928361), (-0.0669556479014, 0.0575695456236, 0.996093714783), (-0.92999934264, -0.365221665633, -0.0414048021585)-11.7194557503, 62.0318219967, -61.9725092792

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Components

#1: Protein
Polyadenylate-binding protein 1 / PABP-1 / Poly(A)-binding protein 1


Mass: 8284.560 Da / Num. of mol.: 8 / Fragment: MLLE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP, PABP1, PABPC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11940
#2: Protein/peptide
superPAM2


Mass: 2431.702 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 4.0, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 27587 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.995 / Net I/σ(I): 17.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 535 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→32.11 Å / SU ML: 0.4259 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.2055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2916 2786 10.1 %
Rwork0.2556 24801 -
obs0.2594 27587 69.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.52 Å2
Refinement stepCycle: LAST / Resolution: 3→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 30 18 4911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164988
X-RAY DIFFRACTIONf_angle_d0.52056823
X-RAY DIFFRACTIONf_chiral_restr0.0338814
X-RAY DIFFRACTIONf_plane_restr0.005892
X-RAY DIFFRACTIONf_dihedral_angle_d2.8665699
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.315882571444
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.74790433198
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.729187862468
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.529140047715
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.468572679653
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.986565604705
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.855249039433
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.986249746496
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.962186155421
ens_2d_5BBX-RAY DIFFRACTIONTorsion NCS1.18582217458
ens_3d_2LLX-RAY DIFFRACTIONTorsion NCS0.703430849723
ens_3d_3LLX-RAY DIFFRACTIONTorsion NCS0.622574590744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.3818210.3654228X-RAY DIFFRACTION12.76
3.05-3.110.3074350.2954293X-RAY DIFFRACTION16.47
3.11-3.170.296460.2815359X-RAY DIFFRACTION21.01
3.17-3.230.2934540.2957452X-RAY DIFFRACTION25.22
3.23-3.30.2824750.2777593X-RAY DIFFRACTION32.97
3.3-3.380.2956940.2771795X-RAY DIFFRACTION45.4
3.38-3.460.35681070.26651069X-RAY DIFFRACTION59.82
3.46-3.560.29791200.27081115X-RAY DIFFRACTION63.59
3.56-3.660.28291390.25681254X-RAY DIFFRACTION68.08
3.66-3.780.30531530.25141347X-RAY DIFFRACTION75.53
3.78-3.910.24671590.25691409X-RAY DIFFRACTION81.5
3.91-4.070.25071850.23241647X-RAY DIFFRACTION89.63
4.07-4.250.2842040.24971749X-RAY DIFFRACTION96.78
4.26-4.480.32841880.24331786X-RAY DIFFRACTION100
4.48-4.760.2962160.24461780X-RAY DIFFRACTION100
4.76-5.120.29591980.26461756X-RAY DIFFRACTION100
5.12-5.640.30931960.26881810X-RAY DIFFRACTION100
5.64-6.440.34221980.2951790X-RAY DIFFRACTION100
6.46-8.10.27072040.26411794X-RAY DIFFRACTION100
8.11-32.110.27241940.22981775X-RAY DIFFRACTION98.94
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)
11.39386439610.20649278136-0.5146982152741.08963246337-0.1422163507722.330675599080.136280283020.00955102006620.07073541633650.2522837318660.07781632651610.191810031397-0.200965051408-0.168413069270.4706295952440.1732472013750.172684290610.1641807490790.3237091603810.0239053259098-0.66190769353151.9480913294-29.6579706065-31.6741248224
21.88925293209-3.75007135655-0.9450724307477.474666117161.705900576481.22740926581-0.0828652930538-0.0966534599674-0.400432715532-0.0418776517136-0.1160070932470.5145353834580.116981225445-0.08956301704710.01427859522860.3219612372990.3696198585570.1164615999560.7504244094670.2228184179690.32883524903445.5074023078-35.7717642792-25.806186982
34.15190499458-2.73343070881.282830954673.97516271154-3.324375769835.695947075520.01099008868440.1870295852050.311919175661-0.374280558247-0.001895724445870.772936577317-0.161342742272-0.403184234688-0.2232742227810.3913557970440.238463601413-0.1455466394460.387955096942-0.05584105668470.56295584537840.3285031981-30.2710896808-41.5932610815
42.14093255621-1.6394438462.263147140127.049694727290.2305398262143.05848068198-0.0658732516796-0.3936538903170.128969816661.165057746620.1472507734691.27757215829-0.0331345484479-0.731558082567-0.07538109503670.7958503728630.4280005533850.02234256847050.889043766919-0.1307971324540.44023954432937.8527197218-25.3598333241-33.9941880839
52.179205936270.434791928373-0.8069635508440.4198280476470.3502519036591.08402962518-0.02795798024770.3026967904890.249279900829-0.216379313578-0.1233934677220.00966861486371-0.345829976406-0.185786242278-0.07413078557990.4536234942620.2640623583550.02784970683080.1890590438370.08881007763640.068007639912353.1385007133-21.8710712578-34.5185534451
65.026325826691.479836078182.771109410757.90388637237-2.044736631732.62282270765-0.0311508001058-1.480918577090.7081150357051.02379368171-0.04168021514230.670636693698-0.514793908982-0.729778114142-0.02376149945510.2474295724340.07844869927960.1958229583770.326856252945-0.03483368960780.26511678532950.2532627013-19.7195937609-27.2855960513
71.66602263087-0.295622202985-0.03516041260920.9187146253970.3687764549311.70987880242-0.0166527088886-0.0263119177147-0.1012664849020.03253355399360.204082242804-0.09102350664820.07375853164930.2263734619180.271098656505-0.0252704131130.155078705610.2590623210.521604192938-0.0824132605507-0.4676636296432.433897694-1.09953802826-62.2736087698
84.459980029750.220661053964-2.066554678080.0170706849539-0.1765003828451.73233933014-0.3197614524650.183913598027-0.551693165824-0.004644637180470.04280386292260.03322947998460.326951157089-0.1143444112610.2751464528280.3083921386150.307740579007-0.03865475190030.674308427644-0.219122773210.284302451190.213636327522-9.79423525506-68.1029184504
92.30687874729-0.506298985170.7849518332371.79774854525-0.1116029469983.0359640570.0609236695478-0.292999780462-0.2639481023120.3358740163050.020722551338-0.6234027165290.1863183523910.221103888576-0.3039540535950.1508720370740.262027985671-0.1224229145310.5296702901850.1875975736150.3166338593428.07076072562-11.2686602524-52.2853334025
106.524880823523.662579989391.039958990838.11284212642-3.196650071982.55737760467-0.2125113829250.9457981954940.12336243482-0.8290426932440.363203932323-0.02401365245871.143238685040.387983756171-0.1056979836240.4784976867070.08091186714520.07276487403030.6833764273890.304907644170.32026709726413.0049157102-10.9968997237-60.1705222293
114.92844245058-3.16713954191-1.845956140963.712307393550.9554094583630.720057863171-0.37606850059-0.299169599473-0.1434317708040.4277612461760.0349328723155-0.006696966449660.1680687894040.3945137606420.05156962878470.220817558701-0.05856741077260.1246324706930.459048746402-0.07920016579160.002020428761988.41585403463.79142645068-59.3578904817
123.676349835380.3394959502082.011114900767.216312100431.387092731723.183176441380.01956449424450.968734066456-0.284854018099-1.257367392040.00315959962855-0.9061996568560.1980800445661.07512496212-0.0616861934850.3428371074680.08066316881150.1811631624560.417702668408-0.1427434181050.25491029602311.94409626172.38054296471-66.7584788424
132.57105338066-1.58371020684-1.824435455773.61583850189-0.7205026470023.752211738620.1334399061440.174082417789-0.340325370932-0.2328717155820.169017384984-0.1126992084530.130782193277-0.0397689334906-0.08527694116590.348243512478-0.0248902379777-0.01056713496550.147783376082-0.09280960680940.27924803063717.9336594136-4.0237659984-24.4775362625
144.70575932376-1.7175584029-1.046495647673.628407861040.5010627111083.365576588140.04461650338710.012391504125-0.3342735212710.2757773819670.01102843450260.1282584256470.109826509618-0.0003683688890270.07835536285020.458530624216-0.0861022159025-0.1353978568360.00167090480914-0.06064984186060.15373954953810.5096319797-4.94978587218-16.431470069
151.20016567767-0.5325142444890.1933973509710.4770809947110.02600718556620.414279038928-0.16547244025-0.1349345168020.1319625308230.0104953794892-0.01499127535030.00226953574722-0.157464376233-0.0368323116703-0.4026045512480.07660212992180.000917218598035-0.2811648677290.273654842668-0.413355310968-0.10502251599328.2589717048-7.64233412572-13.1054610502
169.4665216169-3.958584493622.980559673075.69230865628-2.397304652388.633011641990.4087394140550.519775212077-0.182695490398-0.931803154206-0.2880407447060.6633003038650.2419690767410.275061672773-0.1362595798820.4281457952710.0473748259927-0.1334071110120.250669818155-0.087822219910.38326736649322.6628598267-10.0307431819-24.8132147211
171.00857752478-0.895271392676-0.9593228324620.8040308134660.8914789777081.08106365094-0.09443318808880.165544510239-0.492873778443-0.283229679433-0.1310752003880.336471335670.214719379034-0.1333180411010.2912237162031.292667822820.4027572370990.3372566797730.99689005608-0.5280695522331.3154306233417.9347609952-13.004632262-29.4604930566
187.0203952929-1.27709609433-0.6386122120160.8559426727541.739988859314.286728158820.266214400788-0.3306118869280.2005328537080.458059152254-0.1489825558380.2781403061560.0512968953549-0.282801997497-0.1452735534980.298351031255-0.08418484018250.06407638858770.3713622480340.06070374066950.22768095912141.5286488045-17.7869511365-69.4026255363
191.20103463691-1.155857856520.3369093828411.63438669526-0.5206177879910.7695025720330.124113767320.1893196686660.0905424444516-0.108344471404-0.166196868422-0.0240183950764-0.250370850019-0.0266669328179-0.05269597890430.1638064571740.03703209818830.04151050941950.07499888170860.2897688675670.0091102824967137.2020131744-15.6230775851-79.6773088126
206.61420034626-0.6519277255333.533332876674.90405674808-2.841159599279.128948055380.0192427196127-0.64538394335-0.2669135947460.484942934102-0.02336836854250.206598795762-0.0132635064804-0.127051928289-0.08100589716670.401533971398-0.01515595384730.1392467359950.2885625613480.1204597147610.18577342295734.0570977005-16.6126163654-69.0565504191
211.99997192833-8.38276038766-2.598022781446.536586330562.257190372491.71367774693-0.175336596661-0.0789181324254-0.7996889152520.442465832726-0.2481778651070.9126213235330.438409296255-0.5507952145420.4853008371621.015484294090.1336185072530.679420195711.463596221740.06605138117641.2766617640234.1145673756-21.8933891091-64.6446260385
225.08228124244-0.117286841905-0.9797960086971.552790598310.6542499653281.394054256420.156964858170.203390203457-0.233273942561-0.1124952311630.0531972981552-0.5479752932150.04755062738910.1613240634760.0005067066455680.3867396538550.4701147843770.154124006730.6246651891010.1803570421680.6225038160847.4740720203-20.2229435064-47.8954519483
231.956954646310.3949593291610.2020179447650.3324432073150.4748070706070.7804721079450.576068757397-0.222877486557-1.21690355551-0.181047474737-0.2396262787690.1459339300390.292978009582-0.0835470244586-0.2671710450140.5099138021610.3343174586040.0312055651280.8128391084990.3504083667681.444519791294.94159235052-31.0049865115-42.8987897962
241.174340861060.06617633408760.1659603866050.00422943435630.00767946468930.03396340333790.1126310278690.169430882577-0.1645684254730.2071745152480.21429359165-0.2089207023120.6134312147550.340012473759-0.3026795548141.2080545840.494174175849-0.1067184280151.375441978120.1225123212490.96916416812911.6105281227-36.4133322808-42.3666544121
252.35856144167-0.9293028283080.2302558475490.4230269713390.07146329106980.492912063807-0.0974136418421-0.802452975867-0.8009681522920.3013159705660.3878361915960.573658493420.329930704399-0.243810463924-0.249847237450.5643274342170.330470708536-0.1914429994271.015273989480.4003433567511.3062893584513.1694787521-20.6172437019-39.4820799547
267.200523244840.5893738725942.536363435682.065840733871.997249935615.04109057811-0.102543489096-0.2857158147880.2013674064120.1417550483650.048676514089-0.5892751789030.1225689650210.4833861913480.0413709824570.6173707246020.322814638194-0.32014815550.9135160585860.2182018510570.95678830267317.2236830443-23.3046333012-43.0554809414
272.23028369781-0.202275131040.2381239995641.16030160748-0.7096793406190.9611269922820.115451154719-0.08623239783190.18650439584-0.06069230042810.145504501630.534996867056-0.109641126284-0.46084459028-0.06890366252960.4192297316180.371102191741-0.2818701303010.715883649035-0.1474575501970.91472561380830.7967259066-36.2050561124-48.6349623915
280.463157038994-0.6022001146890.3415463791261.87589688988-0.08892145629970.3558107661840.00811922984025-0.0395652248768-0.494803566871-0.471270501135-0.1009883316911.01823886347-0.0619329900246-0.08287540859960.183836009340.4024177857160.2265377753-0.1516757748561.18849214061-0.2511757374981.5428497618223.3162980955-43.4192921388-50.3062308078
292.069374932821.83244539375-3.551212577392.11587624239-3.559966187526.44415367318-0.1545682069190.248402482508-0.12100339505-0.2049980112930.2047357756220.0975155408170.326943975207-0.452186783991-0.04652828999111.112291905470.0722208281283-0.3193309802591.16997174710.06846733983270.92029227112317.4787932155-38.1852569855-53.2727773929
303.3536787012-1.845647559314.133999354891.03738324083-2.473498546486.898634778870.2171049614720.856630688172-0.33219970062-0.168278767778-0.01596613828790.1868139820940.2550939650990.0674663719175-0.195133680970.790473813650.273767622973-0.6235727037430.8762610922-0.2734647139641.4425453600328.2684404041-32.0314759722-55.2123342104
310.10008183244-0.1061044560030.01370343840310.319240077007-0.1071654776050.04186095187580.02829150979570.04468350023090.0312847151198-0.0365217941007-0.03435916019880.145082031919-0.0588095195506-0.07641300197160.02360295821520.6027737091790.469268873901-0.3815479120930.8831403595040.2859969796980.9759175981531.4646485055-27.3526066822-51.9120109334
329.604956727122.84108639772-0.7761518478575.75262712863-6.075575845527.02007281051-0.699813610483-0.333533690166-0.5360473633110.2605465260960.2645758877270.008914657101610.3169374502720.1512955652580.4083729710160.837472574670.281263094671-0.1854040609920.3633166982510.0810218493381.012634698823.0901366653-26.9591115864-50.8959558705
330.731621139397-0.6828295977360.181433602053.60595621028-0.1037604593381.39674298916-0.3265472668490.0743371861436-0.428393536921-0.0405942018750.133147795431-0.5764465680360.1393010382420.3165713159410.07043288159590.441864309210.0978097653682-0.08059390740381.680093880150.3140410168741.1653086510549.7930213562-0.205187364022-16.0833755375
343.59057666954-3.610050128062.08797667467.304563586523.021574976378.35102255932-0.02551972704230.08155423410810.010586901273-0.05999330715080.0427077641331-0.198972999880.2853671067040.299335120882-0.006926919564640.782224890624-0.1211961155050.248192764741.77629809830.348042106471.1396230986242.4932240016-2.69016316908-21.8448344829
352.081124322381.107568891860.8395434712122.0090973843-1.349730197082.613158306790.0841070037246-0.06659298711930.07307059222170.189672169779-0.269075167513-0.445440283286-0.38732434730.3304377095990.2014781642051.0999272182-0.384220122822-0.03565228509651.082768853670.1892314150271.6237420512553.7216175065.4162128547-23.5736513207
361.30454270745-0.584524575677-0.7269512646521.6082341974-0.694045765031.178318742850.08951290784260.585334946796-0.415415202256-0.168049377656-0.2000305597570.0161235275451-0.0103076107354-0.1057532443260.06447875799281.09542713215-0.0244372977941-0.216303494580.952523868729-0.05027381012531.3654906813637.8446336896-2.29299254275-31.1222145149
376.765790879035.390286970141.900813917565.203473780023.273309214593.94199041253-0.2734746296480.3867889835920.160461452436-0.7878703350150.4099847219370.955859248020.272895049592-0.591838085947-0.1315360446911.04811329729-0.166830247384-0.3573292342311.68105655501-0.006155609580691.7719769956644.6524930199-7.00610165528-30.3007582912
385.642201221212.2257230214-3.585297154582.14878123141-2.296554214372.904585971180.1226682917990.221357259077-0.371043290196-0.136591441701-0.000571812029015-0.1816709274130.3472749305950.214030757019-0.1053615957311.04425717351-0.301094529728-0.5281420866041.494970767850.1627025172721.2387447491445.7160806379-8.54666016399-17.3351373389
393.42578635644-2.03583538177-4.061640664451.523984707782.673663078795.58630464563-0.1963794241430.2948937494570.507723877353-0.176604845648-0.154164478161-0.297790650539-0.5446700935360.7179733574480.3445655278911.055431047320.0997054851604-0.3880458348681.392739406370.6573074106451.2434947496550.7090596345-10.9961046905-17.2269282614
400.565825304870.346056499112-0.07881681997620.9062620000090.379252421261.503577924-0.01890856071310.03765795204740.1891458416190.4415281279340.04495334572730.509644470946-0.1824726859940.006930987716660.008113940321061.345883743850.68590734829-0.1342380270131.044250224750.05118667524931.2511835984428.064318307111.8604392598-77.668786674
414.936363403880.641629563276-0.8498905193676.661689449452.435502715446.29657624759-0.0724397803131-0.1530406240970.347344919902-0.0623381940996-0.253243098490.366825043594-0.1233555480650.02219436056850.3554305784181.465481991320.291070882385-0.1322731201091.33360248499-0.1920686723090.78488079122930.5597422074.06149028733-72.2379803663
422.44208267787-0.3971049732411.611899787226.007381744711.457161959291.56495094211-0.217885597425-0.3052248552770.4866528159940.37600202631-0.2161290945390.184905957242-0.2570646497350.01562066353360.4129403910771.08311598121-0.017567603162-0.2834458605891.15713791646-0.07547705667091.0463093982234.577263027211.680750613-68.3097142587
434.288739626995.5547946948-3.437607687819.57019197076-4.480129767942.762105356890.200219783872-0.192934609524-0.3973295163040.665611134746-0.13942673435-0.7995639697280.08483872398710.436942203851-0.07266895464081.268954529910.392224857686-0.06065963800750.9140996636740.352704007111.0459605677825.61012556493.84792484594-63.7674912156
442.008191591960.850590568259-1.011369206965.406429408553.876099858614.181421592790.0765160982484-0.1167386853650.2118992664570.2102605973060.1707525120510.471414530834-0.259264641592-0.477932992508-0.2243615394021.27067376816-0.233007901398-0.3151475841250.938070291860.5531702390981.239186194123.98700292473.98709498878-76.7036633877
451.043182375610.458584460165-0.7082426402150.27954924024-0.3382356335641.52537727288-0.27222424631-0.3048773157450.02447917486520.391087155227-0.0430236232492-0.259898133683-1.07844875223-0.1668408604350.3032860859511.53277896580.360839488392-0.507156869971.326868130190.6560141923391.7053876216219.42560869437.31693626639-76.8655814511
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 552 through 587 )AA552 - 5871 - 36
22chain 'A' and (resid 588 through 599 )AA588 - 59937 - 48
33chain 'A' and (resid 600 through 625 )AA600 - 62549 - 74
44chain 'B' and (resid 1 through 5 )BB1 - 51 - 5
55chain 'B' and (resid 6 through 15 )BB6 - 156 - 15
66chain 'B' and (resid 16 through 20 )BB16 - 2016 - 20
77chain 'C' and (resid 552 through 587 )CC552 - 5871 - 36
88chain 'C' and (resid 588 through 599 )CC588 - 59937 - 48
99chain 'C' and (resid 600 through 625 )CC600 - 62549 - 74
1010chain 'D' and (resid 1 through 5 )DD1 - 51 - 5
1111chain 'D' and (resid 6 through 15 )DD6 - 156 - 15
1212chain 'D' and (resid 16 through 20 )DD16 - 2016 - 20
1313chain 'E' and (resid 552 through 587 )EE552 - 5871 - 36
1414chain 'E' and (resid 588 through 599 )EE588 - 59937 - 48
1515chain 'E' and (resid 600 through 625 )EE600 - 62549 - 74
1616chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
1717chain 'F' and (resid 16 through 20 )FF16 - 2016 - 20
1818chain 'G' and (resid 552 through 587 )GG552 - 5871 - 36
1919chain 'G' and (resid 588 through 625 )GG588 - 62537 - 74
2020chain 'H' and (resid 1 through 15 )HH1 - 151 - 15
2121chain 'H' and (resid 16 through 19 )HH16 - 1916 - 19
2222chain 'I' and (resid 554 through 573 )II554 - 5731 - 20
2323chain 'I' and (resid 574 through 624 )II574 - 62421 - 71
2424chain 'J' and (resid 1 through 5 )JJ1 - 51 - 5
2525chain 'J' and (resid 6 through 15 )JJ6 - 156 - 15
2626chain 'J' and (resid 16 through 18 )JJ16 - 1816 - 18
2727chain 'K' and (resid 554 through 587 )KK554 - 5871 - 34
2828chain 'K' and (resid 588 through 624 )KK588 - 62435 - 71
2929chain 'L' and (resid 2 through 6 )LL2 - 61 - 5
3030chain 'L' and (resid 7 through 11 )LL7 - 116 - 10
3131chain 'L' and (resid 12 through 16 )LL12 - 1611 - 15
3232chain 'L' and (resid 17 through 18 )LL17 - 1816 - 17
3333chain 'M' and (resid 553 through 573 )MM553 - 5731 - 21
3434chain 'M' and (resid 574 through 587 )MM574 - 58722 - 35
3535chain 'M' and (resid 588 through 603 )MM588 - 60336 - 47
3636chain 'M' and (resid 604 through 621 )MM604 - 62148 - 65
3737chain 'N' and (resid 3 through 7 )NN3 - 71 - 5
3838chain 'N' and (resid 8 through 12 )NN8 - 126 - 10
3939chain 'N' and (resid 13 through 18 )NN13 - 1811 - 16
4040chain 'O' and (resid 552 through 573 )OO552 - 5731 - 22
4141chain 'O' and (resid 574 through 587 )OO574 - 58723 - 36
4242chain 'O' and (resid 588 through 614 )OO588 - 61437 - 61
4343chain 'P' and (resid 3 through 7 )PP3 - 71 - 5
4444chain 'P' and (resid 8 through 12 )PP8 - 126 - 10
4545chain 'P' and (resid 13 through 18 )PP13 - 1811 - 16

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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