Summary Structural details Experimental details Functional details Sequence Neighbor Downloads

1M7W

HNF4a ligand binding domain with bound fatty acid

> Summary

Summary for 1M7W

Descriptor	Hepatocyte nuclear factor 4-alpha
Functional Keywords	transcription factor
Biological source	Rattus rattus (black rat)
Cellular location	Nucleus P22449
Total number of polymer chains	4
Total molecular weight	113283.84
Authors	Dhe-Paganon, S.,Duda, K.,Iwamoto, M.,Chi, Y.I.,Shoelson, S.E. (deposition date: 2002-07-22, release date: 2003-07-01, modification date: 2009-02-24)
Primary citation	Dhe-Paganon, S.,Duda, K.,Iwamoto, M.,Chi, Y.I.,Shoelson, S.E. Crystal structure of the HNF4 alpha ligand binding domain in complex with endogenous fatty acid ligand J.Biol.Chem., 277:37973-37976, 2002 PubMed: 12193589 DOI: 10.1074/jbc.C200420200 Import into Mendeley
Experimental method	X-RAY DIFFRACTION (2.8 Å)

Structure validation

Download full validation report

More Asymmetric unit images

Molmil generated image of 1m7w — no rotation

More Biological unit images

(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.

Coordinate files for Biological unit (1m7w.pdb1.gz [73.88 KB])
Coordinate files for Biological unit (1m7w.pdb2.gz [74.4 KB])
Coordinate files for Biological unit (1m7w.pdb3.gz [288.3 KB])
Coordinate files for Biological unit (1m7w.pdb4.gz [145.26 KB])
Coordinate files for Biological unit (1m7w.pdb5.gz [145.48 KB])
Coordinate files for Biological unit (1m7w.pdb6.gz [145.18 KB])
Coordinate files for Biological unit (1m7w.pdb7.gz [74.06 KB])
Coordinate files for Biological unit (1m7w.pdb8.gz [73.92 KB])

> Structural details

Entity

Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
A, B, C, D	Hepatocyte nuclear factor 4-alpha	polymer	250	28120.6	4	UniProt (P22449) Pfam (PF00104)	Rattus rattus (black rat)	HNF-4-alpha, Transcription factor HNF-4, Transcription factor 14
	LAURIC ACID	non-polymer		200.3	4	DAO
	water	water		18.0	74	HOH

Sequence viewer

Contents of the asymmetric unit

Polymers	Number of chains	4
Polymers	Total molecular weight	112482.6
Non-Polymers*	Number of molecules	4
Non-Polymers*	Total molecular weight	801.3
All*	Total molecular weight	113283.8

*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:

X-RAY DIFFRACTION (2.8 Å)

Cell axes	102.288	102.288	227.688
Cell angles	90.00	90.00	90.00
Spacegroup	P 41 21 2
Resolution limits	20.00 - 2.80
the highest resolution shell value	-
R-work	0.23700 (0.23200*)
R-free	0.28200
RMSD bond length	0.008*
RMSD bond angle	1.350*

Data Collection Statistics

Resolution limits	20.00 - 2.80
the highest resolution shell value	-
Number of reflections	29727
I/sigma(I)	0.5

Crystallization Conditions

crystal ID	method	pH	pH range	temperature	unit
1	Vapor diffusion, sitting drop*	7.5 (8.0*)			R.T.*

Crystallization Reagents

crystal ID

solution ID

reagent name

concentration

details

Crystallization Reagents in Literatures*

ID	crystal ID	solution	reagent name	concentration (unit)	details
1	1	drop	protein	25 (mg/ml)
2	1	reservoir	sodium citrate	0.1 (M)	pH8.0
3	1	reservoir	ammonium acetate	0.7 (M)
4	1	reservoir	MPD	16 (%)
5	1	reservoir	dithiothreitol	10 (mM)

Annotated Information is extracted from Literature Info*

> Functional details

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005634	cellular_component	nucleus
A	0005667	cellular_component	transcription factor complex
A	0003677	molecular_function	DNA binding
A	0005504	molecular_function	fatty acid binding
A	0000062	molecular_function	fatty-acyl-CoA binding
A	0016290	molecular_function	palmitoyl-CoA hydrolase activity
A	0042803	molecular_function	protein homodimerization activity
A	0070491	molecular_function	repressing transcription factor binding
A	0004879	molecular_function	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
A	0043565	molecular_function	sequence-specific DNA binding
A	0003707	molecular_function	steroid hormone receptor activity
A	0003700	molecular_function	transcription factor activity, sequence-specific DNA binding
A	0008134	molecular_function	transcription factor binding
A	0001077	molecular_function	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
A	0008270	molecular_function	zinc ion binding
A	0006637	biological_process	acyl-CoA metabolic process
A	0007568	biological_process	aging
A	0030154	biological_process	cell differentiation
A	0045216	biological_process	cell-cell junction organization
A	0071456	biological_process	cellular response to hypoxia
A	0007164	biological_process	establishment of tissue polarity
A	1902569	biological_process	negative regulation of activation of JAK2 kinase activity
A	0008285	biological_process	negative regulation of cell proliferation
A	0045930	biological_process	negative regulation of mitotic cell cycle
A	0033159	biological_process	negative regulation of protein import into nucleus, translocation
A	0043433	biological_process	negative regulation of sequence-specific DNA binding transcription factor activity
A	0042524	biological_process	negative regulation of tyrosine phosphorylation of Stat5 protein
A	0045723	biological_process	positive regulation of fatty acid biosynthetic process
A	0045722	biological_process	positive regulation of gluconeogenesis
A	0045944	biological_process	positive regulation of transcription from RNA polymerase II promoter
A	0045893	biological_process	positive regulation of transcription, DNA-templated
A	0032534	biological_process	regulation of microvillus assembly
A	0006355	biological_process	regulation of transcription, DNA-templated
A	0051591	biological_process	response to cAMP
A	0042493	biological_process	response to drug
A	0009749	biological_process	response to glucose
B	0005737	cellular_component	cytoplasm
B	0005634	cellular_component	nucleus
B	0005667	cellular_component	transcription factor complex
B	0003677	molecular_function	DNA binding
B	0005504	molecular_function	fatty acid binding
B	0000062	molecular_function	fatty-acyl-CoA binding
B	0016290	molecular_function	palmitoyl-CoA hydrolase activity
B	0042803	molecular_function	protein homodimerization activity
B	0070491	molecular_function	repressing transcription factor binding
B	0004879	molecular_function	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
B	0043565	molecular_function	sequence-specific DNA binding
B	0003707	molecular_function	steroid hormone receptor activity
B	0003700	molecular_function	transcription factor activity, sequence-specific DNA binding
B	0008134	molecular_function	transcription factor binding
B	0001077	molecular_function	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
B	0008270	molecular_function	zinc ion binding
B	0006637	biological_process	acyl-CoA metabolic process
B	0007568	biological_process	aging
B	0030154	biological_process	cell differentiation
B	0045216	biological_process	cell-cell junction organization
B	0071456	biological_process	cellular response to hypoxia
B	0007164	biological_process	establishment of tissue polarity
B	1902569	biological_process	negative regulation of activation of JAK2 kinase activity
B	0008285	biological_process	negative regulation of cell proliferation
B	0045930	biological_process	negative regulation of mitotic cell cycle
B	0033159	biological_process	negative regulation of protein import into nucleus, translocation
B	0043433	biological_process	negative regulation of sequence-specific DNA binding transcription factor activity
B	0042524	biological_process	negative regulation of tyrosine phosphorylation of Stat5 protein
B	0045723	biological_process	positive regulation of fatty acid biosynthetic process
B	0045722	biological_process	positive regulation of gluconeogenesis
B	0045944	biological_process	positive regulation of transcription from RNA polymerase II promoter
B	0045893	biological_process	positive regulation of transcription, DNA-templated
B	0032534	biological_process	regulation of microvillus assembly
B	0006355	biological_process	regulation of transcription, DNA-templated
B	0051591	biological_process	response to cAMP
B	0042493	biological_process	response to drug
B	0009749	biological_process	response to glucose
C	0005737	cellular_component	cytoplasm
C	0005634	cellular_component	nucleus
C	0005667	cellular_component	transcription factor complex
C	0003677	molecular_function	DNA binding
C	0005504	molecular_function	fatty acid binding
C	0000062	molecular_function	fatty-acyl-CoA binding
C	0016290	molecular_function	palmitoyl-CoA hydrolase activity
C	0042803	molecular_function	protein homodimerization activity
C	0070491	molecular_function	repressing transcription factor binding
C	0004879	molecular_function	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
C	0043565	molecular_function	sequence-specific DNA binding
C	0003707	molecular_function	steroid hormone receptor activity
C	0003700	molecular_function	transcription factor activity, sequence-specific DNA binding
C	0008134	molecular_function	transcription factor binding
C	0001077	molecular_function	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
C	0008270	molecular_function	zinc ion binding
C	0006637	biological_process	acyl-CoA metabolic process
C	0007568	biological_process	aging
C	0030154	biological_process	cell differentiation
C	0045216	biological_process	cell-cell junction organization
C	0071456	biological_process	cellular response to hypoxia
C	0007164	biological_process	establishment of tissue polarity
C	1902569	biological_process	negative regulation of activation of JAK2 kinase activity
C	0008285	biological_process	negative regulation of cell proliferation
C	0045930	biological_process	negative regulation of mitotic cell cycle
C	0033159	biological_process	negative regulation of protein import into nucleus, translocation
C	0043433	biological_process	negative regulation of sequence-specific DNA binding transcription factor activity
C	0042524	biological_process	negative regulation of tyrosine phosphorylation of Stat5 protein
C	0045723	biological_process	positive regulation of fatty acid biosynthetic process
C	0045722	biological_process	positive regulation of gluconeogenesis
C	0045944	biological_process	positive regulation of transcription from RNA polymerase II promoter
C	0045893	biological_process	positive regulation of transcription, DNA-templated
C	0032534	biological_process	regulation of microvillus assembly
C	0006355	biological_process	regulation of transcription, DNA-templated
C	0051591	biological_process	response to cAMP
C	0042493	biological_process	response to drug
C	0009749	biological_process	response to glucose
D	0005737	cellular_component	cytoplasm
D	0005634	cellular_component	nucleus
D	0005667	cellular_component	transcription factor complex
D	0003677	molecular_function	DNA binding
D	0005504	molecular_function	fatty acid binding
D	0000062	molecular_function	fatty-acyl-CoA binding
D	0016290	molecular_function	palmitoyl-CoA hydrolase activity
D	0042803	molecular_function	protein homodimerization activity
D	0070491	molecular_function	repressing transcription factor binding
D	0004879	molecular_function	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
D	0043565	molecular_function	sequence-specific DNA binding
D	0003707	molecular_function	steroid hormone receptor activity
D	0003700	molecular_function	transcription factor activity, sequence-specific DNA binding
D	0008134	molecular_function	transcription factor binding
D	0001077	molecular_function	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
D	0008270	molecular_function	zinc ion binding
D	0006637	biological_process	acyl-CoA metabolic process
D	0007568	biological_process	aging
D	0030154	biological_process	cell differentiation
D	0045216	biological_process	cell-cell junction organization
D	0071456	biological_process	cellular response to hypoxia
D	0007164	biological_process	establishment of tissue polarity
D	1902569	biological_process	negative regulation of activation of JAK2 kinase activity
D	0008285	biological_process	negative regulation of cell proliferation
D	0045930	biological_process	negative regulation of mitotic cell cycle
D	0033159	biological_process	negative regulation of protein import into nucleus, translocation
D	0043433	biological_process	negative regulation of sequence-specific DNA binding transcription factor activity
D	0042524	biological_process	negative regulation of tyrosine phosphorylation of Stat5 protein
D	0045723	biological_process	positive regulation of fatty acid biosynthetic process
D	0045722	biological_process	positive regulation of gluconeogenesis
D	0045944	biological_process	positive regulation of transcription from RNA polymerase II promoter
D	0045893	biological_process	positive regulation of transcription, DNA-templated
D	0032534	biological_process	regulation of microvillus assembly
D	0006355	biological_process	regulation of transcription, DNA-templated
D	0051591	biological_process	response to cAMP
D	0042493	biological_process	response to drug
D	0009749	biological_process	response to glucose

Functional Information from PDB Data

site_id

Number of Residues

Details

AC1

BINDING SITE FOR RESIDUE DAO A 700

Chain	Residue
A	SER181
A	GLN185
A	ARG226
A	LEU236
A	GLY237
A	MET252

AC2

BINDING SITE FOR RESIDUE DAO B 701

Chain	Residue
B	HOH30
B	SER181
B	MET182
B	GLN185
B	ARG226
B	LEU236
B	GLY237
B	LEU249
B	MET252

AC3

BINDING SITE FOR RESIDUE DAO C 702

Chain	Residue
C	HOH31
C	VAL178
C	SER181
C	GLN185
C	ALA223
C	ARG226
C	LEU236
C	GLY237
C	MET252
C	ILE259
C	ILE346

AC4

BINDING SITE FOR RESIDUE DAO D 703

Chain	Residue
D	SER181
D	GLN185
D	ARG226
D	LEU236
D	GLY237
D	MET252
D	SER256

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_id

Number of Residues

Details

DAO_1m7w_A_700

LAURIC ACID binding site

Chain	Residue	ligand
A	VAL178	DAO: LAURIC ACID
A	SER181-MET182	DAO: LAURIC ACID
A	GLN185	DAO: LAURIC ACID
A	LEU219-LEU220	DAO: LAURIC ACID
A	ALA223	DAO: LAURIC ACID
A	ARG226	DAO: LAURIC ACID
A	LEU234-GLY237	DAO: LAURIC ACID
A	VAL242	DAO: LAURIC ACID
A	MET252	DAO: LAURIC ACID
A	VAL255-SER256	DAO: LAURIC ACID
A	ILE259	DAO: LAURIC ACID
A	MET342	DAO: LAURIC ACID
A	GLN345-ILE346	DAO: LAURIC ACID
A	ILE349	DAO: LAURIC ACID

DAO_1m7w_B_701

LAURIC ACID binding site

Chain	Residue	ligand
B	VAL178	DAO: LAURIC ACID
B	SER181-MET182	DAO: LAURIC ACID
B	GLN185	DAO: LAURIC ACID
B	LEU219-LEU220	DAO: LAURIC ACID
B	ALA223	DAO: LAURIC ACID
B	ARG226	DAO: LAURIC ACID
B	LEU234-ASN238	DAO: LAURIC ACID
B	VAL242	DAO: LAURIC ACID
B	LEU249	DAO: LAURIC ACID
B	MET252-SER253	DAO: LAURIC ACID
B	VAL255-SER256	DAO: LAURIC ACID
B	ILE259	DAO: LAURIC ACID

DAO_1m7w_C_702

LAURIC ACID binding site

Chain	Residue	ligand
C	ILE175	DAO: LAURIC ACID
C	VAL178-CYS179	DAO: LAURIC ACID
C	SER181-MET182	DAO: LAURIC ACID
C	GLN185	DAO: LAURIC ACID
C	LEU219-LEU220	DAO: LAURIC ACID
C	ALA223	DAO: LAURIC ACID
C	ARG226	DAO: LAURIC ACID
C	LEU234-GLY237	DAO: LAURIC ACID
C	VAL242	DAO: LAURIC ACID
C	LEU249	DAO: LAURIC ACID
C	MET252	DAO: LAURIC ACID
C	VAL255	DAO: LAURIC ACID
C	ILE259	DAO: LAURIC ACID
C	MET342	DAO: LAURIC ACID
C	ILE346	DAO: LAURIC ACID

DAO_1m7w_D_703

LAURIC ACID binding site

Chain	Residue	ligand
D	VAL178	DAO: LAURIC ACID
D	SER181-MET182	DAO: LAURIC ACID
D	GLN185	DAO: LAURIC ACID
D	LEU219-LEU220	DAO: LAURIC ACID
D	ALA223	DAO: LAURIC ACID
D	ARG226	DAO: LAURIC ACID
D	LEU234-GLY237	DAO: LAURIC ACID
D	VAL242	DAO: LAURIC ACID
D	LEU249	DAO: LAURIC ACID
D	MET252	DAO: LAURIC ACID
D	VAL255-SER256	DAO: LAURIC ACID
D	ILE259	DAO: LAURIC ACID
D	MET342	DAO: LAURIC ACID
D	GLN345-ILE346	DAO: LAURIC ACID

Functional Information from PROSITE/UniProt

site_id

Number of Residues

Details

Functional Information from SwissProt/UniProt

site_id

Number of Residues

Details

SWS_FT_FI1

Nuclear receptor.

Chain	Residue	Details
A	NA*

SWS_FT_FI2

Nuclear receptor.

Chain	Residue	Details
B	NA*

SWS_FT_FI3

Nuclear receptor.

Chain	Residue	Details
C	NA*

SWS_FT_FI4

Nuclear receptor.

Chain	Residue	Details
D	NA*

Catalytic Information from CSA

site_id

Number of Residues

Details

Catalytic Information from CATRES

site_id

Number of Residues

Details

> Sequence Neighbor

Sequence navigator - 1m7w: Chain A,B,C,D

> Downloads

Resources

File format		File name (file size)
PDB	all	pdb1m7w.ent.gz (151.27 KB) Display
	all (no-compress)	pdb1m7w.ent (633.92 KB)
	header only	pdb1m7w.ent.gz (8.04 KB) Display
PDBx/mmCIF	1m7w.cif.gz (182.6 KB) Display Flat file Tree view Header
PDBML	all	1m7w.xml.gz (284.03 KB) Display
	no-atom	1m7w-noatom.xml.gz (34.68 KB) Display
	ext-atom	1m7w-extatom.xml.gz (168.91 KB) Display
PDBMLplus	all	1m7w-plus.xml.gz (288.75 KB) Display
	no-atom	1m7w-plus-noatom.xml.gz (39.41 KB) Display
	add only	1m7w-add.xml.gz (4.72 KB) Display
RDF		1m7w.rdf.gz (68.08 KB) Display
Biological unit (PDB format)		1m7w.pdb1.gz (73.88 KB) (A,B) *author defined assembly, 2 molecule(s) (dimeric) Display
		1m7w.pdb2.gz (74.4 KB) (C,D) *author and software defined assembly, 2 molecule(s) (dimeric) Display
		1m7w.pdb3.gz (288.3 KB) (A,B,C,D) *software defined assembly, 8 molecule(s) (octameric) Display
		1m7w.pdb4.gz (145.26 KB) (A,B,C,D) *software defined assembly, 4 molecule(s) (tetrameric) Display
		1m7w.pdb5.gz (145.48 KB) (A,B) *software defined assembly, 4 molecule(s) (tetrameric) Display
		1m7w.pdb6.gz (145.18 KB) (B,C) *software defined assembly, 4 molecule(s) (tetrameric) Display
		1m7w.pdb7.gz (74.06 KB) (B) *software defined assembly, 2 molecule(s) (dimeric) Display
		1m7w.pdb8.gz (73.92 KB) (B,C) *software defined assembly, 2 molecule(s) (dimeric) Display
Validation reports	PDF	1m7w_validation.pdf.gz (249.2 KB) Display
	PDF-full	1m7w_full_validation.pdf.gz (291.75 KB) Display
	XML	1m7w_validation.xml.gz (25.83 KB) Display
	PNG	1m7w_multipercentile_validation.png.gz (118.4 KB) Display
	SVG	1m7w_multipercentile_validation.svg.gz (810 B) Display
Sequence (fasta)	1m7w_seq.txt Display

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123021

entries
(2016-09-28)

123021

entries available on 2016-09-28
00:00 UTC / 09:00 JST

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)