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- PDB-8v14: Structure of NRAP-1 and its role in NMDAR signaling -

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Basic information

Entry
Database: PDB / ID: 8v14
TitleStructure of NRAP-1 and its role in NMDAR signaling
ComponentsNMDA receptor auxiliary protein
KeywordsSIGNALING PROTEIN / NMDAR / NRAP-1 / Synapse / Postsynaptic / Neurotransmitter
Function / homologyLow-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / NMDA receptor auxiliary protein
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWhitby, F.G. / Goodell, D.J. / Maricq, A.V. / Hill, C.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS125359 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS110173 United States
CitationJournal: To Be Published
Title: Functional and Structural Studies of NRAP-1 and NMDAR signaling
Authors: Goodell, D.M. / Maricq, A.V.
History
DepositionNov 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NMDA receptor auxiliary protein
B: NMDA receptor auxiliary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3914
Polymers36,3112
Non-polymers802
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, AUC indicates clearly that the protein is monomeric in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.358, 75.921, 152.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NMDA receptor auxiliary protein


Mass: 18155.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nrap-1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: G5EEF9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.35
Details: 17 mg/mL purified NRAP-1 in 150 mM sodium chloride, 15 mM HEPES, 1 mM calcium chloride, pH 7.35, 1:1 with crystallization solution (26% PEG8000, 100 mM CHES, pH 9.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.12 Å / Num. obs: 38804 / % possible obs: 100 % / Redundancy: 54.8 % / CC1/2: 1 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.015 / Rrim(I) all: 0.112 / Net I/σ(I): 27.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9450.25.36612269724430.8220.7595.421.2100
9.11-38.145.30.047195114310.9990.0070.04781.299.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.106 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1932 5 %RANDOM
Rwork0.1936 ---
obs0.1954 36758 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 194.44 Å2 / Biso mean: 52.871 Å2 / Biso min: 28.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--1.7 Å20 Å2
3----3.13 Å2
Refinement stepCycle: final / Resolution: 1.9→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 2 193 2723
Biso mean--49.26 53.82 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172359
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.6483562
X-RAY DIFFRACTIONr_angle_other_deg1.4531.5795529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5615340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06624.634123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.44158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022998
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02510
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 140 -
Rwork0.316 2675 -
all-2815 -
obs--99.89 %
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)
11.9135-1.9091-1.86372.03642.25654.99580.119-0.0087-0.1556-0.11140.04850.02660.23450.5296-0.16760.0980.0515-0.00040.0945-0.03390.14459.963937.547251.3507
21.465-0.718-0.7261.48091.4774.10490.0646-0.11890.274-0.13720.0426-0.0883-0.60820.0733-0.10720.1035-0.00020.01960.0229-0.01060.065417.978831.169721.1738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 167
2X-RAY DIFFRACTION2B1 - 167

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