[English] 日本語
Yorodumi
- PDB-3ltl: Crystal structure of human BIG1 Sec7 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ltl
TitleCrystal structure of human BIG1 Sec7 domain
ComponentsBrefeldin A-inhibited guanine nucleotide-exchange protein 1
KeywordsSIGNALING PROTEIN / all alpha / Guanine-nucleotide releasing factor
Function / homology
Function and homology information


endomembrane system organization / negative regulation of actin filament polymerization / regulation of ARF protein signal transduction / small nuclear ribonucleoprotein complex / regulation of establishment of cell polarity / negative regulation of GTPase activity / positive regulation of wound healing / myosin binding / protein glycosylation / Golgi organization ...endomembrane system organization / negative regulation of actin filament polymerization / regulation of ARF protein signal transduction / small nuclear ribonucleoprotein complex / regulation of establishment of cell polarity / negative regulation of GTPase activity / positive regulation of wound healing / myosin binding / protein glycosylation / Golgi organization / protein kinase A regulatory subunit binding / exocytosis / guanyl-nucleotide exchange factor activity / trans-Golgi network / nuclear matrix / protein transport / Golgi membrane / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 ...Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Brefeldin A-inhibited guanine nucleotide-exchange protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSimister, P.C. / Joubert, A. / Cherfils, J. / Biou, V.
CitationJournal: To be Published
Title: The Sec7 domain structures of human BIG1 and Cytohesin1 Arf nucleotide exchange factors
Authors: Zeeh, J.C. / Simister, P.C. / Rousseau, V. / Joubert, A. / Cherfils, J. / Biou, V.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Brefeldin A-inhibited guanine nucleotide-exchange protein 1
B: Brefeldin A-inhibited guanine nucleotide-exchange protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9235
Polymers48,7832
Non-polymers1403
Water1,31573
1
A: Brefeldin A-inhibited guanine nucleotide-exchange protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5324
Polymers24,3921
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Brefeldin A-inhibited guanine nucleotide-exchange protein 1


Theoretical massNumber of molelcules
Total (without water)24,3921
Polymers24,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.451, 36.867, 85.848
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Brefeldin A-inhibited guanine nucleotide-exchange protein 1 / Brefeldin A-inhibited GEP 1 / p200 ARF-GEP1 / p200 ARF guanine nucleotide exchange factor


Mass: 24391.643 Da / Num. of mol.: 2 / Fragment: Sec7 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGEF1, ARFGEP1, BIG1 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y6D6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG 3350, 0.2M sodium acetate, 0.2M tris pH 7.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2005
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→80 Å / Num. all: 20705 / Num. obs: 20705 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2870 / Rsym value: 0.509 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PBV

1pbv


Resolution: 2.2→22.605 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1061 5.13 %random
Rwork0.1753 ---
obs0.1785 20674 98.72 %-
all-20674 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.491 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.631 Å20 Å20.3818 Å2
2--1.9943 Å20 Å2
3----2.6253 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 6 73 3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073120
X-RAY DIFFRACTIONf_angle_d0.9984186
X-RAY DIFFRACTIONf_dihedral_angle_d17.3021189
X-RAY DIFFRACTIONf_chiral_restr0.067444
X-RAY DIFFRACTIONf_plane_restr0.003551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.30010.30141260.2287226192
2.3001-2.42120.2751370.19322412100
2.4212-2.57270.25351290.18752489100
2.5727-2.7710.24841380.17112449100
2.771-3.04930.25011100.17912487100
3.0493-3.48910.23941380.17112450100
3.4891-4.39060.19821420.14772502100
4.3906-22.60660.21471410.1627256399
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)
11.3562-0.7482-0.33851.95012.12742.6901-0.1637-0.1330.03010.10020.21750.026-0.00110.7382-0.04450.1871-0.02140.01670.30830.05220.151917.21271.189935.649
21.447-0.43520.36251.0786-0.2441.8054-0.0968-0.01780.07660.07930.00650.0892-0.3801-0.09910.05280.22440.01160.04580.0484-0.03980.1267-3.038712.349330.5667
30.76820.610.31551.5238-0.83311.25750.1184-0.0978-0.19580.33980.23560.7374-0.1289-0.0784-0.36360.32150.04530.08910.16670.02980.3867-14.852414.283823.4305
40.5929-0.74450.23371.1036-0.9083.6996-0.10730.15960.05450.041-0.0537-0.07450.00580.74610.12090.16720.01910.01560.36220.02630.228728.373-4.608417.7954
51.2934-1.18752.00473.0423-1.75465.4607-0.05280.01790.07840.08990.03270.0149-0.2877-0.04750.03940.0492-0.0398-0.00520.12120.04120.117117.70254.0997-0.2467
62.735-0.51021.40060.69570.07022.32520.1584-0.18150.2121-0.16890.0375-0.0329-0.0392-0.2865-0.12110.1511-0.0203-0.04760.16530.03880.21528.11314.8656-9.8512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 697:750)
2X-RAY DIFFRACTION2(chain A and resid 753:847)
3X-RAY DIFFRACTION3(chain A and resid 849:885)
4X-RAY DIFFRACTION4(chain B and resid 697:750)
5X-RAY DIFFRACTION5(chain B and resid 753:847)
6X-RAY DIFFRACTION6(chain B and resid 849:885)

+
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://pdbjlc1.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