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- PDB-1cmi: STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1cmi
TitleSTRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE
Components
  • Dynein light chain 1, cytoplasmic
  • Nitric oxide synthase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / PIN / LC8 / NNOS / DYNEIN LIGHT CHAIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / Nitric oxide stimulates guanylate cyclase / motile cilium assembly / ROS and RNS production in phagocytes / Activation of BIM and translocation to mitochondria / ciliary tip ...nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / Nitric oxide stimulates guanylate cyclase / motile cilium assembly / ROS and RNS production in phagocytes / Activation of BIM and translocation to mitochondria / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / Ion homeostasis / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / dynein intermediate chain binding / synaptic signaling by nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Macroautophagy / negative regulation of calcium ion transport / positive regulation of the force of heart contraction / spermatid development / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / tertiary granule membrane / ficolin-1-rich granule membrane / enzyme inhibitor activity / nitric-oxide synthase (NADPH) / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / xenobiotic catabolic process / striated muscle contraction / regulation of sodium ion transport / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / nitric oxide biosynthetic process / axon cytoplasm / Mitotic Prometaphase / substantia nigra development / T-tubule / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / sarcoplasmic reticulum membrane / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / calyx of Held / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / establishment of localization in cell / RHO GTPases Activate Formins / sarcolemma / potassium ion transport / kinetochore / cellular response to growth factor stimulus / Z disc / HCMV Early Events / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / calcium ion transport / Regulation of PLK1 Activity at G2/M Transition / FMN binding / flavin adenine dinucleotide binding / NADP binding / site of double-strand break / scaffold protein binding / dendritic spine / microtubule / cytoskeleton / calmodulin binding / cilium / membrane raft / apoptotic process / synapse / heme binding / centrosome / DNA damage response / Neutrophil degranulation / protein-containing complex binding / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / PDZ domain / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLiang, J. / Guo, W. / Jaffery, S. / Snyder, S. / Clardy, J.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure of the PIN/LC8 dimer with a bound peptide.
Authors: Liang, J. / Jaffrey, S.R. / Guo, W. / Snyder, S.H. / Clardy, J.
History
DepositionMay 6, 1999Deposition site: BNL / Processing site: RCSB
SupersessionFeb 21, 2000ID: 1B1W
Revision 1.0Feb 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
C: Nitric oxide synthase 1
D: Nitric oxide synthase 1


Theoretical massNumber of molelcules
Total (without water)22,7384
Polymers22,7384
Non-polymers00
Water36020
1
A: Dynein light chain 1, cytoplasmic
C: Nitric oxide synthase 1


Theoretical massNumber of molelcules
Total (without water)11,3692
Polymers11,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynein light chain 1, cytoplasmic
D: Nitric oxide synthase 1


Theoretical massNumber of molelcules
Total (without water)11,3692
Polymers11,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.200, 67.200, 217.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.713023, -0.698246, 0.06367), (-0.701095, -0.711139, 0.052642), (0.008513, -0.082178, -0.996587)38.23158, 96.34148, 22.67481
2given(0.713023, -0.698246, 0.06367), (-0.701095, -0.711139, 0.052642), (0.008513, -0.082178, -0.996587)38.23158, 96.34148, 22.67481

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Components

#1: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal ...8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal nitric oxide synthase / PIN


Mass: 9875.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Plasmid: PGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63167
#2: Protein/peptide Nitric oxide synthase 1 / Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Nitric oxide synthase / ...Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Nitric oxide synthase / brain / bNOS / Peptidyl-cysteine S-nitrosylase NOS1


Mass: 1493.705 Da / Num. of mol.: 2 / Fragment: RESIDUE 225-237 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9Z0J4, nitric-oxide synthase (NADPH)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.69 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mM1dropNaN3
416 %mPEG20001reservoir
510 %MPD1reservoir
60.2 M1reservoirMgCl2
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9792, 0.9790, 0.964
DetectorType: ADSC / Detector: CCD / Date: Apr 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.9791
30.9641
ReflectionResolution: 2.5→20 Å / Num. obs: 9052 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLORCNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1454419.65 / Data cutoff low absF: 0 / Cross valid method: FREE-R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 446 5 %RANDOM
Rwork0.24 ---
obs-9000 99.7 %-
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å20 Å2
2--2.75 Å20 Å2
3----5.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 0 20 1596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTSX-RAY DIFFRACTION2100
22X-RAY DIFFRACTION2100
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 79 5.4 %
Rwork0.314 1373 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: 'X-PLOR CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59

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