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- PDB-6ype: Crystal structure of the human neuronal pentraxin 1 (NP1) pentrax... -

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Basic information

Entry
Database: PDB / ID: 6ype
TitleCrystal structure of the human neuronal pentraxin 1 (NP1) pentraxin (PTX) domain.
ComponentsNeuronal pentraxin-1
KeywordsCELL ADHESION / synapse formation / AMPA receptor
Function / homology
Function and homology information


regulation of postsynaptic neurotransmitter receptor activity / axonogenesis involved in innervation / transport vesicle / central nervous system development / chemical synaptic transmission / neuron projection / glutamatergic synapse / metal ion binding / plasma membrane
Similarity search - Function
Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / Neuronal pentraxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsElegheert, J. / Clayton, A.J. / Aricescu, A.R.
Funding support3items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0065/2014
Medical Research Council (MRC, United Kingdom)L009609
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15
CitationJournal: Science / Year: 2020
Title: A synthetic synaptic organizer protein restores glutamatergic neuronal circuits.
Authors: Suzuki, K. / Elegheert, J. / Song, I. / Sasakura, H. / Senkov, O. / Matsuda, K. / Kakegawa, W. / Clayton, A.J. / Chang, V.T. / Ferrer-Ferrer, M. / Miura, E. / Kaushik, R. / Ikeno, M. / ...Authors: Suzuki, K. / Elegheert, J. / Song, I. / Sasakura, H. / Senkov, O. / Matsuda, K. / Kakegawa, W. / Clayton, A.J. / Chang, V.T. / Ferrer-Ferrer, M. / Miura, E. / Kaushik, R. / Ikeno, M. / Morioka, Y. / Takeuchi, Y. / Shimada, T. / Otsuka, S. / Stoyanov, S. / Watanabe, M. / Takeuchi, K. / Dityatev, A. / Aricescu, A.R. / Yuzaki, M.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuronal pentraxin-1
B: Neuronal pentraxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8348
Polymers45,3992
Non-polymers4346
Water8,575476
1
A: Neuronal pentraxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9174
Polymers22,7001
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuronal pentraxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9174
Polymers22,7001
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.220, 36.060, 92.170
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neuronal pentraxin-1 / NP1 / Neuronal pentraxin I / NP-I


Mass: 22699.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPTX1 / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q15818
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% (v/v) glycerol, 25.5% (w/v) polyethylene glycol (PEG) 8000, 0.17M ammonium sulphate, 0.085 M sodium cacodylate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→45.694 Å / Num. obs: 69831 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.054 / Rrim(I) all: 0.103 / Net I/σ(I): 11.7
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4824 / CC1/2: 0.495 / Rpim(I) all: 0.599 / Rrim(I) all: 1.021 / % possible all: 94.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev-2645refinement
XDSdata reduction
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SAC

1sac


Resolution: 1.45→45.694 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.06
RfactorNum. reflection% reflection
Rfree0.178 3556 5.09 %
Rwork0.1531 --
obs0.1544 69824 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.9 Å2 / Biso mean: 15.0658 Å2 / Biso min: 4.2 Å2
Refinement stepCycle: final / Resolution: 1.45→45.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 14 476 3673
Biso mean--15.85 28.85 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053381
X-RAY DIFFRACTIONf_angle_d0.8814631
X-RAY DIFFRACTIONf_chiral_restr0.081496
X-RAY DIFFRACTIONf_plane_restr0.006592
X-RAY DIFFRACTIONf_dihedral_angle_d14.651197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.46990.31711440.2964241692
1.4699-1.49090.24011460.2768255496
1.4909-1.51310.26671600.2469263099
1.5131-1.53680.26931550.2313261599
1.5368-1.5620.24551230.22132685100
1.562-1.58890.2391430.2109261799
1.5889-1.61780.2221390.2008267799
1.6178-1.64890.21421420.19442657100
1.6489-1.68260.20081560.18392612100
1.6826-1.71920.20161530.1704268799
1.7192-1.75920.1921360.1618259499
1.7592-1.80320.19421200.1534273599
1.8032-1.85190.18571510.1442257999
1.8519-1.90640.1381350.14252716100
1.9064-1.96790.15381450.1344263999
1.9679-2.03830.16241450.12552658100
2.0383-2.11990.14151410.1221266099
2.1199-2.21640.13421350.12392665100
2.2164-2.33320.1451360.1251269999
2.3332-2.47940.16841480.1268262999
2.4794-2.67080.16191480.1329268199
2.6708-2.93950.17981250.1351268999
2.9395-3.36480.1591390.144269699
3.3648-4.23880.16991450.1305265797
4.2388-45.6940.17161460.1667282199
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)
10.0563-0.0897-0.04350.17750.04640.05190.0634-0.04830.0123-0.0329-0.0296-0.14180.03090.09560.02970.0823-0.0206-0.01660.1320.02530.1049-2.72320.2907-28.413
20.12740.06490.01510.0626-0.0220.16390.0372-0.0089-0.02530.0132-0.0288-0.00530.0133-0.00100.0748-0.0081-0.01160.05790.00080.0611-15.976121.7917-30.2873
30.0227-0.00410.00970.02630.00430.0244-0.0104-0.0799-0.07480.1815-0.01080.14730.0411-0.07130.00380.0968-0.01220.00160.09570.01660.0788-24.190116.402-28.6663
40.34670.07490.10670.3658-0.02170.30750.0282-0.0302-0.03150.0305-0.0037-0.02390.0007-0.00400.0623-0.0077-0.00020.05140.00270.0589-17.758920.4387-36.4054
50.04470.00520.02090.0507-0.11030.31430.02520.09390.0424-0.0031-0.0473-0.0874-0.09490.28360.01840.0858-0.0172-0.00470.12630.00680.1095-3.277524.7249-37.622
60.0039-0.00240.03980.1643-0.14460.59720.0191-0.01640.0546-0.01280.06690.1520.1557-0.13440.05520.0658-0.0045-0.01420.1135-0.00110.1064-53.59137.0815-15.5381
70.2179-0.0130.06770.20590.01330.13780.02460.0928-0.0117-0.01240.0221-0.00730.0090.012900.0585-0.0021-0.00150.0678-0.00170.0614-38.48168.6088-15.0376
80.2171-0.00390.25950.0325-0.03280.3350.06110.0748-0.10930.01210.02290.03830.14360.01990.07330.1213-0.0106-0.0240.0496-0.02150.1184-39.718-4.2929-9.0965
90.44370.15820.01840.4001-0.14690.1795-0.00360.0553-0.02930.00840.0124-0.00430.0095-0.008200.05080.00090.0070.0483-0.00270.0488-37.39178.9867-8.7661
100.49340.27650.45260.3785-0.01040.7250.0282-0.11240.08470.0439-0.02350.0946-0.0552-0.27610.03210.04280.02290.02110.10360.01090.1007-52.205811.8668-6.0066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 225:242)A225 - 242
2X-RAY DIFFRACTION2(chain A and resid 243:289)A243 - 289
3X-RAY DIFFRACTION3(chain A and resid 290:303)A290 - 303
4X-RAY DIFFRACTION4(chain A and resid 304:399)A304 - 399
5X-RAY DIFFRACTION5(chain A and resid 400:429)A400 - 429
6X-RAY DIFFRACTION6(chain B and resid 225:242)B225 - 242
7X-RAY DIFFRACTION7(chain B and resid 243:301)B243 - 301
8X-RAY DIFFRACTION8(chain B and resid 302:311)B302 - 311
9X-RAY DIFFRACTION9(chain B and resid 312:399)B312 - 399
10X-RAY DIFFRACTION10(chain B and resid 400:429)B400 - 429

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