[English] 日本語
Yorodumi
- PDB-4i1q: Crystal Structure of hBRAP1 N-BAR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i1q
TitleCrystal Structure of hBRAP1 N-BAR domain
ComponentsBridging integrator 2
KeywordsCELL ADHESION / N-BAR MEMBRANE BINDING DOMAIN / PIX and Endophilin A2
Function / homology
Function and homology information


plasma membrane tubulation / podosome assembly / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / podosome / anchoring junction / phagocytic cup / phagocytosis, engulfment / cell chemotaxis / cell projection / phospholipid binding ...plasma membrane tubulation / podosome assembly / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / podosome / anchoring junction / phagocytic cup / phagocytosis, engulfment / cell chemotaxis / cell projection / phospholipid binding / cell cortex / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular region / plasma membrane
Similarity search - Function
: / : / Bridging integrator 2, C-terminal / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily ...: / : / Bridging integrator 2, C-terminal / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bridging integrator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.53 Å
AuthorsSanchez-Barrena, M.J.
CitationJournal: Plos One / Year: 2012
Title: Bin2 Is a Membrane Sculpting N-BAR Protein That Influences Leucocyte Podosomes, Motility and Phagocytosis
Authors: Sanchez-Barrena, M.J. / Vallis, Y. / Clatworthy, M.R. / Doherty, G.J. / Veprintsev, D.B. / Evans, P.R. / McMahon, H.T.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bridging integrator 2
B: Bridging integrator 2


Theoretical massNumber of molelcules
Total (without water)52,1272
Polymers52,1272
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-26 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.147, 81.278, 81.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 41 - 237 / Label seq-ID: 24 - 220

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Bridging integrator 2 / / Breast cancer-associated protein 1


Mass: 26063.312 Da / Num. of mol.: 2 / Fragment: N-BAR domain, UNP residues 20-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIN2 / Plasmid: PGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5alpha / References: UniProt: Q9UBW5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 48 ASN IS NATURAL VARIANT (RS7312857).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 10% MPD, 7% PEG 4000, 0.1M sodium citrate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9791
SYNCHROTRONESRF ID2920.9791, 0.9792, 0.9756
SYNCHROTRONESRF ID2930.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 7, 2006
ADSC QUANTUM 42CCDOct 7, 2006
ADSC QUANTUM 43CCDOct 7, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1liquid nitrogen cooled channel-cut silicon monochromatorSINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled channel-cut silicon monochromatorMADMx-ray1
3liquid nitrogen cooled channel-cut silicon monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97921
30.97561
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.888
11K, H, -L20.112
ReflectionResolution: 2.53→57.41 Å / Num. all: 15899 / Num. obs: 15899 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 59.298 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.9
Reflection shellResolution: 2.53→2.73 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2323 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
REFMAC5.7.0024refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.53→57.41 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.582 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 860 5.4 %RANDOM
Rwork0.19587 ---
all0.19891 14986 --
obs0.19891 14986 87.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.786 Å2
Baniso -1Baniso -2Baniso -3
1-8.91 Å20 Å20 Å2
2---5.93 Å2-0 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.53→57.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 0 62 3393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193391
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9424558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62125.179195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40915655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2221520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022588
Refine LS restraints NCS

Ens-ID: 1 / Number: 244 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.25 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.528→2.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 7 -
Rwork0.229 71 -
obs-71 5.95 %

+
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