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- PDB-2m0c: Solution NMR Structure of Homeobox Domain of Human ALX4, Northeas... -

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Basic information

Entry
Database: PDB / ID: 2m0c
TitleSolution NMR Structure of Homeobox Domain of Human ALX4, Northeast Structural Genomics Consortium (NESG) Target HR4490C
ComponentsHomeobox protein aristaless-like 4
KeywordsGENE REGULATION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / muscle organ development / anterior/posterior pattern specification / embryonic digit morphogenesis / roof of mouth development / hair follicle development ...HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / muscle organ development / anterior/posterior pattern specification / embryonic digit morphogenesis / roof of mouth development / hair follicle development / post-embryonic development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like ...OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein aristaless-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXu, X. / Eletsky, A. / Pulavarti, S. / Lee, D. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Homeobox Domain of Human ALX4, Northeast Structural Genomics Consortium (NESG) Target HR4490C
Authors: Xu, X. / Eletsky, A. / Pulavarti, S. / Lee, D. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 24, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox protein aristaless-like 4


Theoretical massNumber of molelcules
Total (without water)9,3571
Polymers9,3571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein aristaless-like 4 /


Mass: 9356.658 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding residues 209-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALX4, KIAA1788 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9H161

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC ali
1313D HNCO
141(4,3)D GFT CABCA(CO)NH
1512D 1H-13C HSQC aro
161(4,3)D GFT HNCABCA
1713D simultaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY ali
1111(4,3)D GFT (H)CCH-COSY ali
1121(4,3)D GFT (H)CCH-COSY aro
11312D 15N HSQC His
11422D 13C CT-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.871 mM [U-100% 13C; U-100% 15N] HR4490C, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM Tris-HCl, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [5% 13C; U-100% 15N] HR4490C, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM Tris-HCl, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.871 mMHR4490C-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTris-HCl-51
50 uMDSS-61
0.6 mMHR4490C-7[5% 13C; U-100% 15N]2
100 mMsodium chloride-82
5 mMDTT-92
0.02 %sodium azide-102
10 mMTris-HCl-112
50 uMDSS-122
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionedata analysis
AS-DP1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
PROSAGuntertdata analysis
CSIWishart and Sykesdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD
NMR constraintsNOE constraints total: 841 / NOE intraresidue total count: 188 / NOE long range total count: 205 / NOE medium range total count: 232 / NOE sequential total count: 216 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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