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1zzi

Crystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA

Method: X-RAY DIFFRACTION Dmax: 63.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Heterogeneous nuclear ribonucleoprotein K

Homo sapiens

UniProt P61978

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain A； UniProt 385–463 Fragment：KH3 domain 5'-D(*CP*TP*CP*CP*CP*C)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；PEG 4000, TRIS HCl, MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 1.80 Å R-free 0.240
2 Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain B； UniProt 385–463 Fragment：KH3 domain 5'-D(*CP*TP*CP*CP*CP*C)-3' × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；PEG 4000, TRIS HCl, MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 1.80 Å R-free 0.240

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1ZZI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J5K COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER DNA OLIGONUCLEOTIDE Deposited 2002-05-13 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 379–463（85 aa） Fragment：KH3 domain, RESIDUES 379-463, NUMBERED 5-89
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE
Resolution not provided
1KHM C-TERMINAL KH DOMAIN OF HNRNP K (KH3) Deposited 1999-01-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 375–463（89 aa） Fragment：C-TERMINAL KH DOMAIN, RESIDUES 379-463 OF FULL LENGTH HNRNP K
Mutation：G26R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；300 K；Ionic strength (raw mmCIF value) 5 mM；Pressure 1
Resolution not provided
1ZZJ Structure of the third KH domain of hnRNP K in complex with 15-mer ssDNA Deposited 2005-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 385–463（79 aa） Fragment：KH3 domain
Chain B 385–463（79 aa） Fragment：KH3 domain
Chain C 385–463（79 aa） Fragment：KH3 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；PEG 8000, SODIUM ACETATE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.30 Å R-free 0.283
1ZZK Crystal Structure of the third KH domain of hnRNP K at 0.95A resolution Deposited 2005-06-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 385–463（79 aa） Fragment：KH3 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；ammonium sulphate, PEG 400, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 0.95 Å R-free 0.127
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–38（21 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000
Resolution 2.80 Å R-free 0.240
7CRU hnRNPK NLS in complex with Importin alpha 1 (KPNA2) Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 18–38（21 aa）
Not recorded ACT ACETATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 17% w/v PEG 10000
Resolution 2.80 Å R-free 0.240
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 57–66（10 aa） Fragment：UNP residues 57-66
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate
Resolution 1.85 Å R-free 0.217
7RJK Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 57–66（10 aa） Fragment：UNP residues 57-66
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium/sodium tartrate tetrahydrate
Resolution 1.85 Å R-free 0.217
7RJO Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 57–66（10 aa） Fragment：UNP residues 57-66
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris
Resolution 1.38 Å R-free 0.198

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HNRPK_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 4–82； UniProt 385–463 Author chain B； PDBConstruct 4–82； UniProt 385–463

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1zzi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zzi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zzi
Deposition date deposition_date2005-06-14
Structure title titleCrystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA
Keywords keywordsPROTEIN-ssDNA COMPLEX, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.83 Å
Radius of gyration Rg (electron density) rg_electron18.77 Å
Forward intensity I(0) i09270120.00
Molecular weight molecular_weight20718.0 kDa
Excluded volume excluded_volume25188 ų
Envelope volume envelope_volume31330 ų
Hydration-shell volume shell_volume14691 ų
Envelope diameter envelope_diameter65.8 Å
Shell Rg shell_rg23.75 Å
Envelope Rg envelope_rg18.90 Å
Shape Rg shape_rg18.73 Å
Total Rg total_rg19.62 Å
Total atoms total_atoms1444
Residues n_residues173
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.9 Å
Rg (real space) rg_real19.87 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real9.2700e+06
I(0) uncertainty (real space) i0_real_error1.1400e+05
Rg (reciprocal space) rg_reciprocal19.87 Å
I(0) (reciprocal space) i0_reciprocal9270000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.8 Å
Skewness Skewness skewness0.319
Kurtosis Kurtosis kurtosis-0.616
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1088000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.974
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1zzia2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamilyd.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family familyd.51.1.0 — automated matches
Domain ID domain_idd1zzia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1zzib_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamilyd.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family familyd.51.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id1zziA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id1zziB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
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8. Citations (1)

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9. Files and Curves (10)