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- PDB-5uwj: Crystal Structure of FMRP NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uwj
TitleCrystal Structure of FMRP NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
  • Synaptic functional regulator FMR1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / dendritic filopodium / regulation of translation at presynapse, modulating synaptic transmission / host-mediated perturbation of viral RNA genome replication / poly(G) binding / histone H3 reader activity / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / regulation of neuronal action potential ...positive regulation of intracellular transport of viral material / dendritic filopodium / regulation of translation at presynapse, modulating synaptic transmission / host-mediated perturbation of viral RNA genome replication / poly(G) binding / histone H3 reader activity / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / regulation of neuronal action potential / negative regulation of voltage-gated calcium channel activity / animal organ development / negative regulation of long-term synaptic depression / regulation of dendritic spine development / RNA strand annealing activity / filopodium tip / chromocenter / positive regulation of long-term neuronal synaptic plasticity / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / regulation of filopodium assembly / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / regulation of neurotransmitter secretion / cellular response to mineralocorticoid stimulus / negative regulation of synaptic vesicle exocytosis / Regulation of cholesterol biosynthesis by SREBP (SREBF) / N6-methyladenosine-containing RNA reader activity / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / protein localization to kinetochore / poly(A) binding / siRNA binding / positive regulation of proteasomal protein catabolic process / membraneless organelle assembly / spindle pole body / Rev-mediated nuclear export of HIV RNA / growth cone filopodium / sequence-specific mRNA binding / Nuclear import of Rev protein / regulatory ncRNA-mediated gene silencing / U4 snRNA binding / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / miRNA binding / nuclear import signal receptor activity / positive regulation of filopodium assembly / poly(U) RNA binding / MicroRNA (miRNA) biogenesis / intracellular membraneless organelle / glutamate receptor signaling pathway / DNA metabolic process / regulation of alternative mRNA splicing, via spliceosome / MAPK6/MAPK4 signaling / positive regulation of dendritic spine development / dynein intermediate chain binding / dynein complex binding / mitotic sister chromatid segregation / positive regulation of receptor internalization / ribosomal large subunit export from nucleus / U5 snRNA binding / chromosome, centromeric region / glial cell projection / spermatid development / viral process / U2 snRNA binding / mRNA transport / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / mRNA export from nucleus / ribosomal subunit export from nucleus / U1 snRNA binding / Cajal body / negative regulation of cytoplasmic translation / ribosomal small subunit export from nucleus / translation regulator activity / translation initiation factor binding / translation repressor activity / signaling adaptor activity / axon terminus / negative regulation of translational initiation / regulation of mRNA stability / centriole / stress granule assembly / GTPase activator activity
Similarity search - Function
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain ...Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / KH domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / K Homology domain / K homology RNA-binding domain / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.221 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, Hong Kong, 7items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)International Student Research Fellowship United States
Croucher FoundationPredoc Research Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
University of Texas Southwestern Medical CenterEndowed Scholars Program United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352, RP150053 United States
CitationJournal: Elife / Year: 2017
Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.
Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Synaptic functional regulator FMR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4819
Polymers162,6584
Non-polymers8235
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-56 kcal/mol
Surface area58040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.493, 106.493, 303.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26758.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Synaptic functional regulator FMR1


Mass: 1919.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q06787*PLUS

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Non-polymers , 4 types, 579 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 10 mM spermine-HCl, 4 mM HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 86622 / % possible obs: 99.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Net I/σ(I): 21.6
Reflection shellResolution: 2.22→2.26 Å / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4266 / CC1/2: 0.669 / Rpim(I) all: 0.408 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HB2

4hb2


Resolution: 2.221→47.625 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1852 2.15 %
Rwork0.1803 --
obs0.181 86185 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.221→47.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10890 0 18 574 11482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411290
X-RAY DIFFRACTIONf_angle_d0.63115304
X-RAY DIFFRACTIONf_dihedral_angle_d15.3176868
X-RAY DIFFRACTIONf_chiral_restr0.041748
X-RAY DIFFRACTIONf_plane_restr0.0041947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2212-2.28130.28241350.24176084X-RAY DIFFRACTION95
2.2813-2.34840.3031400.22786353X-RAY DIFFRACTION99
2.3484-2.42420.24381420.21916472X-RAY DIFFRACTION100
2.4242-2.51090.28741420.20876446X-RAY DIFFRACTION100
2.5109-2.61140.2341420.19476459X-RAY DIFFRACTION100
2.6114-2.73020.20561420.19126476X-RAY DIFFRACTION100
2.7302-2.87420.25491430.19066485X-RAY DIFFRACTION100
2.8742-3.05420.25681410.19566487X-RAY DIFFRACTION100
3.0542-3.290.20821430.18666514X-RAY DIFFRACTION100
3.29-3.62090.23361410.18026535X-RAY DIFFRACTION99
3.6209-4.14460.19151440.15836558X-RAY DIFFRACTION99
4.1446-5.22080.15591460.14096622X-RAY DIFFRACTION99
5.2208-47.6360.1791510.17526842X-RAY DIFFRACTION97
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)
12.0486-0.6037-0.08413.4114-0.59482.90530.10140.4095-0.0952-0.43360.0669-0.5029-0.27870.3268-0.14390.1881-0.05490.08670.3395-0.11450.34577.522945.760229.5672
22.9643-2.5043-0.78277.46631.38953.10790.20480.17860.1189-0.07130.1222-1.009-0.59130.6925-0.34780.262-0.11550.04850.4035-0.12590.468611.802753.036337.9831
34.7271-1.07541.08581.5227-0.49419.08790.05530.3287-0.7085-0.2979-0.0932-0.36090.73780.23480.03110.19830.01850.02210.328-0.13380.586611.231532.509234.8891
43.0569-0.1532-0.61041.9676-0.70951.53520.05360.1925-0.01230.22240.1169-0.4326-0.020.4497-0.07460.1313-0.0043-0.02170.2134-0.09170.31894.642.637739.5754
52.0985-1.890.35914.2455-3.02956.860.07710.1178-0.2631-0.2201-0.0225-0.25360.52510.101-0.08390.1220.0138-0.00170.197-0.07850.2979-1.532534.1438.6317
63.8411-0.52840.04454.8889-0.37185.2572-0.3712-0.52480.01880.55010.1277-0.2494-0.24910.02060.25040.1680.0185-0.01370.199-0.07290.31891.564943.469543.8452
71.72160.3327-1.03523.1134-1.25363.98490.03770.25180.0866-0.40460.03590.17880.1261-0.3777-0.07930.17940.0301-0.05940.2722-0.06140.2327-8.169345.426634.1289
80.98880.8701-1.18231.64-1.46681.75290.07880.23890.4210.1280.32670.0386-1.06310.6523-0.36250.525-0.21780.03570.4652-0.09160.38476.89262.566237.7801
97.49316.4093-0.7746.0645-1.05970.34750.2881-0.12480.5013-0.56830.7639-1.259-0.64940.9981-0.91720.7789-0.27580.26371.3374-0.43770.774919.369463.01794.6886
106.3475-1.1291-2.67142.02930.45145.3279-0.4515-0.1374-0.03250.06570.59880.56470.27830.0632-0.1370.4851-0.09590.1590.3721-0.09040.6562-0.633356.377311.2969
110.13050.1044-0.05060.27370.79263.58660.08520.03380.3212-0.00230.42560.0493-0.63760.542-0.52811.1024-0.18760.08010.7640.06260.75892.146282.395651.0307
124.9715-1.05160.39159.12971.9514.12190.07240.03060.00250.09180.0877-0.15-0.39860.6183-0.18360.3703-0.15790.11280.40350.02820.28436.999563.147517.3553
130.90070.49360.02931.1942-0.14010.0588-0.08280.0730.1211-0.01290.04220.073-1.05660.72060.11890.735-0.30330.16560.465-0.02070.45767.443171.33519.4699
144.4563.48870.0434.72530.94960.5884-0.21410.26680.2182-0.43950.28540.1379-0.9310.6869-0.01450.6872-0.26550.12570.5126-0.0210.39187.825871.288913.7305
151.6154-0.0622-0.0442.25210.48761.3779-0.1164-0.1359-0.05220.61020.2831-0.81270.38130.3872-0.03630.22830.1386-0.25190.3402-0.08870.566410.03224.832152.8369
161.3003-0.92420.82811.5809-0.96853.14240.0033-0.00880.05340.06140.0748-0.0048-0.1968-0.3036-0.07770.20510.00970.02670.2881-0.06390.163-25.498452.698549.3108
171.9345-0.0954-0.32152.13760.41562.79360.16050.00460.2862-0.2050.0858-0.0263-0.8632-0.527-0.21260.53060.22290.09130.45750.11060.2587-33.342762.71619.8052
181.5154-1.12410.08091.9032-0.15291.21450.01610.1294-0.0938-0.09940.10390.0378-0.0732-0.0003-0.11920.2299-0.00710.04050.3168-0.03850.1701-15.812239.68430.7768
191.4961-0.73210.99871.5404-0.96543.09460.1610.0633-0.3648-0.22260.03680.32710.3105-0.0868-0.13250.20040.00340.00040.2182-0.06080.3567-6.924610.519920.5545
202.05112.9399-3.84939.1959-3.13538.38930.3258-0.33611.2452-0.40140.21381.152-0.9821-0.5293-0.52051.33370.40320.24960.73810.01340.7186-38.893776.329328.171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 158 )
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 190 )
9X-RAY DIFFRACTION9chain 'A' and (resid 191 through 205 )
10X-RAY DIFFRACTION10chain 'A' and (resid 206 through 216 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 82 )
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 154 )
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 200 )
15X-RAY DIFFRACTION15chain 'C' and (resid -1 through 245 )
16X-RAY DIFFRACTION16chain 'C' and (resid 246 through 569 )
17X-RAY DIFFRACTION17chain 'C' and (resid 570 through 692 )
18X-RAY DIFFRACTION18chain 'C' and (resid 693 through 897 )
19X-RAY DIFFRACTION19chain 'C' and (resid 898 through 1053 )
20X-RAY DIFFRACTION20chain 'D' and (resid 427 through 437 )

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