[English] 日本語
Yorodumi
- PDB-5g4p: Crystal structure of human hippocalcin at 2.4 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g4p
TitleCrystal structure of human hippocalcin at 2.4 A resolution
ComponentsNeuron-specific calcium-binding protein hippocalcin
KeywordsCALCIUM BINDING PROTEIN / CA BINDING PROTEIN / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


response to ketamine / regulation of voltage-gated calcium channel activity / response to Aroclor 1254 / cellular response to electrical stimulus / cellular response to L-glutamate / neuronal cell body membrane / dendritic spine head / regulation of postsynaptic neurotransmitter receptor internalization / inner ear development / positive regulation of protein targeting to membrane ...response to ketamine / regulation of voltage-gated calcium channel activity / response to Aroclor 1254 / cellular response to electrical stimulus / cellular response to L-glutamate / neuronal cell body membrane / dendritic spine head / regulation of postsynaptic neurotransmitter receptor internalization / inner ear development / positive regulation of protein targeting to membrane / regulation of signal transduction / dendrite membrane / dendrite cytoplasm / cellular response to calcium ion / calcium-mediated signaling / kinase binding / retina development in camera-type eye / actin binding / perikaryon / axon / calcium ion binding / glutamatergic synapse / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Recoverin family / EF hand domain / EF-hand domain pair / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Neuron-specific calcium-binding protein hippocalcin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsAntonyuk, S.V. / Helassa, N. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D.
CitationJournal: Hum. Mol. Genet. / Year: 2017
Title: Biophysical and functional characterization of hippocalcin mutants responsible for human dystonia.
Authors: Helassa, N. / Antonyuk, S.V. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D.
History
DepositionMay 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuron-specific calcium-binding protein hippocalcin
E: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1478
Polymers44,9072
Non-polymers2406
Water61334
1
A: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5744
Polymers22,4531
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Neuron-specific calcium-binding protein hippocalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5744
Polymers22,4531
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.970, 50.970, 284.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A6 - 188
2114E6 - 188

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.866381, 0.488524, -0.10358), (-0.489584, -0.871797, -0.016675), (-0.098447, 0.036265, 0.994481)-1.75082, 4.80396, 23.27215

-
Components

#1: Protein Neuron-specific calcium-binding protein hippocalcin / Calcium-binding protein BDR-2


Mass: 22453.402 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPCA, BDR2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84074
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.5, 18% V/V 2-PROPANOL, 16% W/V PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.42→43.56 Å / Num. obs: 15734 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.07
Reflection shellResolution: 2.42→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AEQ

5aeq


Resolution: 2.42→47.43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 36.292 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27685 770 4.9 %RANDOM
Rwork0.22519 ---
obs0.22766 14886 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.609 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-1.28 Å20 Å2
2---2.56 Å20 Å2
3---8.29 Å2
Refinement stepCycle: 1 / Resolution: 2.42→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 6 34 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023068
X-RAY DIFFRACTIONr_bond_other_d0.0020.022808
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9674082
X-RAY DIFFRACTIONr_angle_other_deg1.04436490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43124.675154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.271519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.483.2271477
X-RAY DIFFRACTIONr_mcbond_other2.4813.2231476
X-RAY DIFFRACTIONr_mcangle_it3.1814.8081834
X-RAY DIFFRACTIONr_mcangle_other3.184.8131835
X-RAY DIFFRACTIONr_scbond_it3.3243.3441591
X-RAY DIFFRACTIONr_scbond_other3.3233.3481592
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6684.8982249
X-RAY DIFFRACTIONr_long_range_B_refined8.80330.33913091
X-RAY DIFFRACTIONr_long_range_B_other8.80330.34413092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2815 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.670.5
medium thermal4.922
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 62 -
Rwork0.362 1057 -
obs--99.29 %
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)
11.0505-0.91560.71122.8293-0.71311.88280.22860.21040.1639-0.1517-0.5329-0.1593-0.02960.46950.30440.58430.13740.06150.73860.12130.0599.7257.0430.046
20.990.04330.69910.2840.35513.5787-0.454-0.25470.05160.1099-0.15960.13910.0899-0.5940.61360.73130.06880.05750.6503-0.10920.1356-8.8773.014-24.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 188
2X-RAY DIFFRACTION2E5 - 189

+
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