[English] 日本語
Yorodumi
- PDB-2h61: X-ray structure of human Ca2+-loaded S100B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h61
TitleX-ray structure of human Ca2+-loaded S100B
Components(Protein S100-B) x 2
KeywordsMETAL BINDING PROTEIN / SIGNALING PROTEIN / S100 / EF-hand / Calcium-binding / RAGE
Function / homology
Function and homology information


adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation ...adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / S100 protein binding / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / axonogenesis / central nervous system development / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / calcium-dependent protein binding / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOstendorp, T. / Heizmann, C.W. / Kroneck, P.M.H. / Fritz, G.
CitationJournal: Embo J. / Year: 2007
Title: Structural and functional insights into RAGE activation by multimeric S100B.
Authors: Ostendorp, T. / Leclerc, E. / Galichet, A. / Koch, M. / Demling, N. / Weigle, B. / Heizmann, C.W. / Kroneck, P.M. / Fritz, G.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The crystals of S100B were dissolved and checked by reversed phase HPLC and mass ...SEQUENCE The crystals of S100B were dissolved and checked by reversed phase HPLC and mass spectrometry. It was found that about 30% of the N-terminal Met in S100B was post translationally modified by E.coli. The mass deviation is in agreement with FME.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein S100-B
B: Protein S100-B
C: Protein S100-B
D: Protein S100-B
E: Protein S100-B
F: Protein S100-B
G: Protein S100-B
H: Protein S100-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,81627
Polymers85,9008
Non-polymers91619
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20680 Å2
ΔGint-407 kcal/mol
Surface area32160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.400, 81.600, 71.500
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe assymetric unit contains four homodimers which associate to two tetramers, which combine to an octamer

-
Components

#1: Protein
Protein S100-B / S100 calcium-binding protein B / S-100 protein beta subunit / S-100 protein beta chain


Mass: 10727.037 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: MET at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEMEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04271
#2: Protein Protein S100-B


Mass: 10755.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: FME at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEMEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04271
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M HEPES, 18-20%PEG400, 0.2 M CaCl2, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 63871 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.9 / Num. unique all: 7334 / % possible all: 94.1

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MHO

1mho


Resolution: 1.9→30.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.638 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3.54 / ESU R: 0.169 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2743 5 %RANDOM
Rwork0.174 ---
all0.177 ---
obs-54870 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.07 Å2
2---0.53 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 31 617 6565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216034
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9538062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78226.469337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.899158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024534
X-RAY DIFFRACTIONr_nbd_refined0.230.23349
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2632
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.228
X-RAY DIFFRACTIONr_mcbond_it1.4841.53733
X-RAY DIFFRACTIONr_mcangle_it1.7325787
X-RAY DIFFRACTIONr_scbond_it3.19232536
X-RAY DIFFRACTIONr_scangle_it4.6344.52275
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 200 -
Rwork0.208 3798 -
obs-3998 100 %
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)
12.98271.59770.05983.98480.10171.3056-0.02020.06110.15810.0225-0.035-0.25930.08550.0710.0553-0.15270.02260.0480.07030.0313-0.05862.1994.08546.381
21.19490.0024-0.69591.5731.00544.8617-0.18380.1661-0.132-0.1213-0.037-0.05840.6341-0.11310.22080.0095-0.02180.09430.0423-0.0134-0.1111-3.625-12.45734.71
31.23470.26850.00992.94630.15690.77760.067-0.23270.10370.4363-0.07550.1530.0080.0870.0085-0.055-0.02270.04550.0963-0.0153-0.0886-1.614-15.04170.308
44.1867-3.44250.08774.8649-0.17020.51070.16660.0580.0593-0.2997-0.1113-0.08760.08660.0585-0.0553-0.09440.00610.02490.05460.013-0.10425.654-29.6357.994
51.2605-0.5476-0.4912.20232.2994.2351-0.04380.1648-0.21570.0962-0.04340.14190.2816-0.01540.0872-0.1523-0.02250.05720.0883-0.0097-0.061-23.469-32.42152.117
62.40910.2568-2.33862.06260.92195.8872-0.02360.12690.05190.14060.00560.21390.0498-0.66310.018-0.17750.00170.06990.16010.0427-0.0718-32.714-22.23267.018
72.61391.31822.50452.32021.49013.56660.09280.195-0.3119-0.2240.1574-0.1320.0550.1581-0.2502-0.1060.02410.01470.0629-0.0466-0.0819-34.152-10.98833.249
82.3002-0.61860.1373.55860.69781.6787-0.06760.00190.18530.12930.1571-0.0502-0.06860.0942-0.0896-0.15030.01540.00060.0832-0.01-0.0825-30.4652.51147.823
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 89 / Label seq-ID: 1 - 90

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF
77GG
88HH

+
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