[English] 日本語
Yorodumi
- PDB-2rcb: Crystal structure of the NR3B ligand binding core complex with D-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rcb
TitleCrystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom resolution
ComponentsGlutamate [NMDA] receptor subunit 3B
KeywordsMEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


neurotransmitter receptor activity / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / glycine binding / monoatomic cation transmembrane transport / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine ...neurotransmitter receptor activity / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / glycine binding / monoatomic cation transmembrane transport / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / calcium ion transmembrane transport / presynaptic membrane / postsynaptic membrane / neuronal cell body / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Periplasmic binding protein-like I ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-SERINE / Glutamate receptor ionotropic, NMDA 3B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsYao, Y. / Mayer, M.L.
Citation
Journal: Embo J. / Year: 2008
Title: Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.
Authors: Yao, Y. / Harrison, C.B. / Freddolino, P.L. / Schulten, K. / Mayer, M.L.
#1: Journal: J.NEUROSCI. / Year: 2006
Title: Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A
Authors: Yao, Y. / Mayer, M.L.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN ...RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN FROM THE UNP entry Q8VHN2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate [NMDA] receptor subunit 3B
B: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6645
Polymers64,3612
Non-polymers3023
Water8,557475
1
A: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3783
Polymers32,1811
Non-polymers1972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2862
Polymers32,1811
Non-polymers1051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.779, 83.521, 144.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is believed to be a dimer of dimers. In the present structure packing is not biologically relevant

-
Components

#1: Protein Glutamate [NMDA] receptor subunit 3B / N-methyl-D-aspartate receptor subtype 3B / NR3B / NMDAR3B


Mass: 32180.646 Da / Num. of mol.: 2 / Fragment: unp residues 413-560, 676-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: Peptides corresponding to A413-R560 and E676-K815 were coupled by a GT dipeptid e synthetic linker
Gene: Grin3b / Plasmid: pET22b(+) modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB (DE3) / References: UniProt: Q8VHN2
#2: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M NaCitrate, 17% PEG 4000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2006
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→40 Å / Num. all: 71657 / Num. obs: 71657 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.5
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.96 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.3.0038refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb entry 1PB7

1pb7


Resolution: 1.62→36.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.529 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22754 5525 7.8 %RANDOM
Rwork0.19178 ---
all0.19455 65305 --
obs0.19455 65305 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.293 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 20 475 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9656273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9075584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14822.574202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041537
X-RAY DIFFRACTIONr_chiral_restr0.1080.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.32161
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.53282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5751
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40422939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98834642
X-RAY DIFFRACTIONr_scbond_it1.74521876
X-RAY DIFFRACTIONr_scangle_it2.47331630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 400 -
Rwork0.196 4683 -
obs--97.73 %
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)
11.94870.5998-0.04221.0432-0.27912.0860.06870.27690.1934-0.05350.05710.2271-0.2563-0.2692-0.12590.00790.03290.0220.08970.02560.076641.101626.039211.4856
21.13270.0106-0.06510.7172-0.34271.41350.1273-0.04890.0460.0808-0.1029-0.0575-0.14560.1796-0.02440.0369-0.05280.0280.074-0.01290.065256.979522.702421.8742
30.9461-0.1624-0.16472.0877-0.59371.33790.1219-0.1208-0.01910.0825-0.0821-0.0149-0.06460.1568-0.03980.0294-0.05680.00760.09460.0030.057956.83417.582726.1783
40.9392-1.0871-0.56085.81382.49272.3027-0.0289-0.24790.14210.09920.094-0.2415-0.1737-0.0639-0.0650.0647-0.0010.07440.0399-0.04830.042244.462732.133433.9531
51.1086-0.35850.16712.04810.29981.4761-0.072-0.1232-0.03090.33630.0318-0.35410.1160.27460.04020.090.0696-0.03510.04150.04760.036862.4872-14.726822.0383
61.0056-0.6134-0.01011.8786-0.53960.82890.0082-0.0146-0.0583-0.2783-0.00590.07170.1784-0.0122-0.00230.0960.0073-0.02030.03570.00320.037848.7869-8.2276.0049
70.9003-0.6231-0.06153.29410.95890.87160.13170.06220.0503-0.3957-0.1176-0.08140.1013-0.0474-0.01410.11430.0334-0.00430.01380.01370.030148.97532.05695.6374
81.3139-0.93390.10352.4226-0.41290.8097-0.1155-0.2075-0.2243-0.00960.10610.35810.1782-0.08480.00940.061-0.00210.01310.04050.02520.057345.9466-16.079314.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 574 - 57
2X-RAY DIFFRACTION2AA58 - 19258 - 192
3X-RAY DIFFRACTION3AA193 - 266193 - 266
4X-RAY DIFFRACTION4AA267 - 285267 - 285
5X-RAY DIFFRACTION5BB4 - 1024 - 102
6X-RAY DIFFRACTION6BB103 - 170103 - 170
7X-RAY DIFFRACTION7BB171 - 216171 - 216
8X-RAY DIFFRACTION8BB217 - 285217 - 285

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more