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- PDB-9cb5: Crystal structure of nucleolin in complex with MYC promoter G-qua... -

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Basic information

Entry
Database: PDB / ID: 9cb5
TitleCrystal structure of nucleolin in complex with MYC promoter G-quadruplex
Components
  • Fab heavy chain
  • Fab light chain
  • MYC promoter G-quadruplex
  • Nucleolin
KeywordsTRANSCRIPTION/DNA / MYC G-quadruplex / Nucleolin / modular protein / transcription factor / G4-epigenetic / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


macropinosome membrane / DNA topoisomerase binding / PH domain binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cornified envelope / positive regulation of mRNA splicing, via spliceosome / telomeric DNA binding / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / Major pathway of rRNA processing in the nucleolus and cytosol ...macropinosome membrane / DNA topoisomerase binding / PH domain binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cornified envelope / positive regulation of mRNA splicing, via spliceosome / telomeric DNA binding / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of insulin receptor signaling pathway / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / spliceosomal complex / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / chromosome / cell cortex / angiogenesis / negative regulation of translation / ribonucleoprotein complex / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Nucleolin, RNA recognition motif 1 / Nucleolin, RNA recognition motif 2 / Nucleolin, RNA recognition motif 3 / Nucleolin, RNA recognition motif 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Nucleolin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, L. / Dickerhoff, J. / Noinaj, N. / Yang, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA177585 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA240346 United States
CitationJournal: Science / Year: 2025
Title: Structural basis for nucleolin recognition of MYC promoter G-quadruplex.
Authors: Chen, L. / Dickerhoff, J. / Zheng, K.W. / Erramilli, S. / Feng, H. / Wu, G. / Onel, B. / Chen, Y. / Wang, K.B. / Carver, M. / Lin, C. / Sakai, S. / Wan, J. / Vinson, C. / Hurley, L. / ...Authors: Chen, L. / Dickerhoff, J. / Zheng, K.W. / Erramilli, S. / Feng, H. / Wu, G. / Onel, B. / Chen, Y. / Wang, K.B. / Carver, M. / Lin, C. / Sakai, S. / Wan, J. / Vinson, C. / Hurley, L. / Kossiakoff, A.A. / Deng, N. / Bai, Y. / Noinaj, N. / Yang, D.
History
DepositionJun 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleolin
B: Nucleolin
C: MYC promoter G-quadruplex
D: Fab heavy chain
F: MYC promoter G-quadruplex
G: Fab heavy chain
H: Fab light chain
I: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,44012
Polymers194,2848
Non-polymers1564
Water3,405189
1
A: Nucleolin
F: MYC promoter G-quadruplex
G: Fab heavy chain
I: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2206
Polymers97,1424
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-46 kcal/mol
Surface area32200 Å2
MethodPISA
2
B: Nucleolin
C: MYC promoter G-quadruplex
D: Fab heavy chain
H: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2206
Polymers97,1424
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-47 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.253, 134.660, 185.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 4 molecules DGHI

#3: Antibody Fab heavy chain


Mass: 26722.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab light chain


Mass: 23152.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / DNA chain , 2 types, 4 molecules ABCF

#1: Protein Nucleolin / Protein C23


Mass: 38462.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19338
#2: DNA chain MYC promoter G-quadruplex


Mass: 8803.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 193 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 20% PEG 8000, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.6→48.43 Å / Num. obs: 56511 / % possible obs: 96.77 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.88 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.094 / Rrim(I) all: 0.246 / Rsym value: 0.226 / Net I/σ(I): 7.38
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 3575 / CC1/2: 0.21 / Rpim(I) all: 0.858 / Rrim(I) all: 2.17 / Rsym value: 1.985 / % possible all: 87.34

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.43 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1999 3.54 %
Rwork0.2323 --
obs0.2331 56511 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9064 1072 4 189 10329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210472
X-RAY DIFFRACTIONf_angle_d0.55614464
X-RAY DIFFRACTIONf_dihedral_angle_d18.5223744
X-RAY DIFFRACTIONf_chiral_restr0.041617
X-RAY DIFFRACTIONf_plane_restr0.0041682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.41311260.39243449X-RAY DIFFRACTION96.2
2.67-2.740.4321410.35423820X-RAY DIFFRACTION96
2.74-2.820.33491390.33073787X-RAY DIFFRACTION96
2.82-2.910.3481400.31713810X-RAY DIFFRACTION95
2.91-3.020.31361390.30693803X-RAY DIFFRACTION95
3.02-3.140.34021400.30373803X-RAY DIFFRACTION95
3.14-3.280.32481400.26563835X-RAY DIFFRACTION96
3.28-3.450.26711410.2343874X-RAY DIFFRACTION97
3.45-3.670.26461460.22233970X-RAY DIFFRACTION99
3.67-3.950.22571470.21184000X-RAY DIFFRACTION99
3.95-4.350.21371450.18843968X-RAY DIFFRACTION99
4.35-4.980.17991490.16874035X-RAY DIFFRACTION99
4.98-6.270.22921500.2034082X-RAY DIFFRACTION100
6.27-48.430.19881560.20584276X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.4735 Å / Origin y: -15.3436 Å / Origin z: 7.8566 Å
111213212223313233
T0.2241 Å2-0.0372 Å2-0.0262 Å2-0.2517 Å2-0.003 Å2--0.3826 Å2
L0.481 °2-0.0222 °2-0.3094 °2-0.3484 °2-0.0474 °2--1.141 °2
S0.0379 Å °-0.0538 Å °0.169 Å °0.0651 Å °-0.0028 Å °-0.1357 Å °-0.2479 Å °0.0719 Å °-0.0135 Å °
Refinement TLS groupSelection details: all

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