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PDB ID Mentions in PubMed Central Article count: 10

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PDB ID Mentions in PubMed Central

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Structure-guided alterations of the gp41-directed HIV-1 broadly neutralizing antibody 2F5 reveal new properties regarding its neutralizing function.

(2012) PLoS Pathog 8

PubMed: 22829767 | PubMedCentral: PMC3400562 | DOI: 10.1371/journal.ppat.1002806

(B) Model of the HIV spike with gp120 (green) bound to the antibody 17b (orange), the primary virus receptor CD4 (yellow) (PDB:2NXY) and the MPER (modified from PDB:3G9R) (red [2F5 eptitope], blue [4E... 0 epitope] and yellow) bound to the antibody 2F5 (black) with the wt CDRH3 (magenta) positioned within the groove between two of the MPER helices.

Publication Year: 2012


Computer-aided antibody design.

(2012) Protein Eng Des Sel 25

PubMed: 22661385 | PubMedCentral: PMC3449398 | DOI: 10.1093/protein/gzs024

Then, they determined the crystal structures, demonstrating the similarity between the inserted epitope in the scaffold and the epitope recognized by 4E10 in the antibody–peptide crystal struc... ures.

Publication Year: 2012


An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.

(2013) PLoS Biol 11

PubMed: 23382649 | PubMedCentral: PMC3558466 | DOI: 10.1371/journal.pbio.1001472

Accession Codes The atomic coordinates and the structure factors for all crystal structures reported here have been deposited in the Protein Data Bank with accession codes 4E0G, 4E0J, 4E0P, 4DWP, 4E10... 4E0Z, and 4E0Y.

TelA/DNAa+VO 4 3− R255A/DNAa TelA/DNAb SeMet-TelA/DNAc Y201A/DNAb R205A/DNAb6 TelA/DNAd Hairpin Product Unligated Hairpin p-Tyr Complex Trapped with a Nick p-Tyr Complex (Se) Trapped with a Nick Mutant Complex Mutant Complex p-Tyr Complex Trapped with a Mismatch Protein Data Bank ID 4E0G 4E0J 4E0P 4DWP 4E10 4E0Z 4E0Y Beamline APS 24-ID-C APS 24-ID-C APS 14-BM-C APS 14-ID-B APS 24-ID-C APS 24-ID-C APS 24-ID-C Data collection Space group C2 C2 C2 C2 C2 C2 C2 Cell dimensions a,b,c (Å) 117.88, 120.20, 58.04 117.56, 120.08, 56.76 117.58, 119.69, 62.94, 117.85, 119.77, 65.98, 116.34, 119.66, 56.63 117.27, 120.39, 58.72 116.98, 119.44, 56.92 β (°) 111.85 111.68 113.94 108.63 111.30 112.46 112.42 Wavelength (Å) 0.979 0.979 0.900 0.979 0.979 0.979 0.979 Resolution (Å) 50–2.20 (2.24–2.20) 50–2.30 (2.34–2.30) 50–2.20 (2.24–2.20) 50–2.35 (2.39–2.35) 50–2.40 (2.44–2.40) 50–2.42 (2.46–2.42) 50–2.40 (2.44–2.40) R sym (%) 7.8 (38.2) 9.5 (20.0) 6.4 (19.9) 8.3 (23.7) 4.6 (23.2) 7.0 (25.5) 6.7 (34.3) I/σ(I) 13.5 (4.0) 22.17 (5.15) 22.5 (3.9) 24.4 (5.1) 15.7 (1.6) 15.5 (4.7) 14.1 (3.0) Completeness (%) 99.2 (98.8) 88.2 (65.2) 94.5 (83.2) 83.6 (52.9) 88.2 (72.6) 87.0 (60.0) 98.8 (98.1) Redundancy 3.3 (3.1) 3.4 (3.0) 6.4 (5.1) 6.4 (4.5) 2.0 (1.7) 3.2 (2.9) 3.2 (2.9) Phasing (25–3.2 Å) Sites 11 FOM 0.49 Refinement Resolution (Å) 50–2.20 50–2.30 50–2.20 50–2.35 50–2.50 50–2.42 50–2.40 Anisotropic resol.

Publication Year: 2013


MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.

(2013) BMC Bioinformatics 14

PubMed: 23718826 | PubMedCentral: PMC3687570 | DOI: 10.1186/1471-2105-14-168

We also briefly explored the efficacy of using the MAPs database to support antibody engineering and design using two broadly neutralizing antibodies: the anti-influenza antibody CH65 (PDB: 3sm5) [ 46... ] and the anti-HIV antibody 4E10 (PDB: 2fx7) [ 47 ].

Publication Year: 2013


Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses.

(2013) PLoS One 8

PubMed: 24039745 | PubMedCentral: PMC3765159 | DOI: 10.1371/journal.pone.0072205

With known X-ray crystallographic structures of the 4E10 Fab bound to a number of cognate epitope peptides, we juxtaposed the LWNWFDITNW 4E10-peptide complex structure (PDB ID 2FX7) with that of the V... 2 puff region of HRV14 ( Figure 4 ) to design a third library aimed at conserving the integrity of the structure of both the HIV epitope and HRV.

g003 Figure 3 Docking of HRV14 (shown in yellow) with a crystallographic structure (1TZG from the Protein Data Bank) of a complex of the 4E10 Fab (orange) complexed with the cognate Ac-KGWNWFDITNWGK-NH 2 peptide (blue ribbon and gold stick-and-balls model).

Publication Year: 2013


Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10.

(2013) PLoS Pathog 9

PubMed: 24086134 | PubMedCentral: PMC3784475 | DOI: 10.1371/journal.ppat.1003639

pdb) 4E10 Fv are shown; HCDR1 and 3 are shown in cartoon representations with side-chains of key residues shown in licorice-stick representations and labeled.

( B ) Superposition of residues from the 4E10 epitope binding site and HCDR1 and 3 from bound (semi-transparent molecular surface in pink; 2FX7.

Because the residues involved in inferred CL contacts in this site all make important contributions to the overall structure of 4E10 in the complex structures, cleanly interpretable mutagenesis studies could not be performed.

The 4E10 Fv in the unbound state was crystallized from Li 2 SO 4 (d min  = 2.4 Å), preliminary phases were determined by molecular replacement, and the structure was rebuilt and refined with good agreement statistics and geometry ( Table 1 ).

pdb [110] and 4E10 (2FX7.

( E ) The structure of the unbound form of 4E10 (4LLV.

Crystal structures of 4E10/epitope peptide complexes [8] – [10] , [34] limited how 4E10 might interact with lipids, liposomes or membranes ( Fig. 11A ).

The previously available 4E10 crystal structures, determined as complexes with epitope ligands, did reveal a potential phosphate binding site, between the side-chains of K32L and K100eH, albeit in the absence of a crevice or groove complementary to a full CL headgroup.

The crystal structure of 4E10 free of bound ligands showed a dramatic restructuring of the combining site, occluding the HIV epitope binding site and revealing profound flexibility, but creating an electropositive pocket consistent with non-specific binding of phospholipid headgroups.

Outside of the K32L/K100eH site, inspection of available 4E10 structures, which were all determined as complexes with HIV epitope-related ligands, failed to reveal any obvious electropositive pocket, crevice or groove that might be reasonably inferred to confer CL binding, so no further targeted mutagenesis studies were performed.

Comparison of the presumed solution-state, unbound 4E10 conformer, using the better-ordered dyad mate, with a reference epitope-peptide 4E10 Fab complex structure (2FX7.

Initial phase information was determined by molecular replacement with Phaser [96] , as implemented in the CCP4i program suite [97] , a previous bound 4E10 structure (3H3P.

pdb [104] ; 4E10: 2FX7.

( F ) CL is shown docked onto the unbound structure of 4E10 oriented and colored as in ( E ).

Publication Year: 2013


Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies.

(2014) Bioinformatics 30

PubMed: 24930144 | PubMedCentral: PMC4173008 | DOI: 10.1093/bioinformatics/btu194

Among these, we found a newly solved structure of the 4E10 antibody (PDB ID: 4LLV) that was already present in the training set (PDB ID: 2FX7) that we excluded from our analysis.

Publication Year: 2014


Ontogeny of recognition specificity and functionality for the broadly neutralizing anti-HIV antibody 4E10.

(2014) PLoS Pathog 10

PubMed: 25254371 | PubMedCentral: PMC4177983 | DOI: 10.1371/journal.ppat.1004403

pdb), unbound 4E10 (4LLV.

pdb), unbound 4E10 (4LLV.

pdb, in complex with ES T88) in purple, 4E10 Fab (2FX7.

On the left in both frames is shown the superposition of V H domains from ligand-bound 4E10 (3LH2.

pdb, with green HCDRs) vs. unbound 4E10 (4LLV.

Previous crystal structures of 4E10/ES complexes showed that many ESs achieved this goal well, including T93 [15] , [55] .

( B ) The NWFDIT core epitope is shown in a licorice stick representation isolated from the superimposed complex structures, highlighting the high degree of conservation of both the position and conformation of the peptide across 4E10 and GEP complexes.

Materials and Methods Protein prediction, expression, purification and characterization The 4E10 heavy and light chain nucleotide sequences were analyzed using JoinSolver [63] , IMGT/V-QUEST [64] , [65] , Ab-Origin [66] , SoDA [67] and iHMMune [68] to compositely identify segments with the fewest nucleotide mismatches, generating a combinatorial ensemble of 12 GEPs ( Fig. 1 ).

Supporting Information Movie S1 Superposition of epitope binding site contacts from bound and unbound forms of 4E10.

( A ) Residues from the combining sites of 4E10 and GEPs, superimposed based on bound-state structures, contacting the NWFDIT core epitope (shown in a cartoon representation as a grey corkscrew) are shown in a stereo view.

( A ) Superpositions of the V H domains from two 4E10 ligand-bound structures (2FX7.

Residue P14H in each Fv, chosen as a reference point to illustrate interdomain movement upon binding between 4E10 and GEPs, is shown as a sphere and colored to match the corresponding backbone.

Ligand Analyte Results (RU) Concentration Range Injection Time (s) Dissociation Time (s) Regeneration k a (M −1 s −1 ) k d (s −1 ) K D (M) T117 129 4E10 10 - 0.625 nM 420 180 or 7200 2×10 s, pH 1.5 9.35(2)×10 5 2.65(1)×10 −5 2.83(1)×10 −11 T117 129 GEP 1 50 - 3.12 nM 420 600 5 s, pH 1.5 4.56(2)×10 5 1.80(1)×10 −3 3.96(2)×10 −9 T117 183 GEP 2 50 - 1.56 nM 420 600 5 s, pH 2.0 5.90(1)×10 5 1.52(1)×10 −3 2.57(1)×10 −9 T117 86 GEP 3 50 - 0.78 nM 420 600 5 s, pH 1.75 5.43(1)×10 5 1.56(1)×10 −3 2.88(1)×10 −9 T117 129 GEP 4 400 - 12.5 nM 420 600 5 s, pH 1.5 6.90(4)×10 4 1.54(1)×10 −3 2.23(1)×10 −8 T117 129 GEP 6 20 - 0.625 µM 180 300 none 5.61(3)×10 3 2.58(1)×10 −3 4.60(3)×10 −7 T117 183 GEP 7 25 - 1.56 nM 420 600 5 s, pH 2.0 6.31(2)×10 5 1.30(1)×10 −3 2.06(1)×10 −9 T117 86 GEP 8 25 - 1.56 nM 420 600 5 s, pH 1.75 9.18(2)×10 5 1.63(1)×10 −3 1.78(1)×10 −9 T117 122 GEP 1 m 25 - 0.78 nM 420 600 2×10 s, pH 1.5 5.33(1)×10 5 7.47(1)×10 −4 1.40(1)×10 −9 T72 30 4E10 10 - 0.312 nM 420 800 10 s, pH 1.5 1.54(1)×10 6 3.36(1)×10 −4 2.19(1)×10 −10 T72 30 GEP 1 45 - 0.088 µM 120 180 none 1.4(1)×10 −6 T72 53 GEP 2 9.5 - 0.149 µM 120 180 none 1.25(6)×10 −6 T72 53 GEP 3 10 - 0.078 µM 120 180 none 1.78(4)×10 −6 T72 53 GEP 4 20 - 0.625 µM 300 300 10 s, pH 1.5 7.9(5)×10 −6 T72 30 GEP 6 1 µM 120 180 none None detected T72 30 GEP 7 17 - 0.066 µM 120 180 none 1.34(5)×10 −6 T72 53 GEP 8 20 - 0.156 µM 120 180 none 1.26(6)×10 −6 T93 49 4E10 10 - 0.625 nM 420 800 10 s, pH 1.5 8.22(1)×10 5 4.21(1)×10 −4 5.13(1)×10 −10 T93 75 GEP 1 50 - 0.098 µM 120 180 none 9.3(1)×10 −6 T93 49 GEP 2 50 - 0.098 µM 120 180 none 5.1(7)×10 −6 T93 27 GEP 3 10 - 0.156 µM 120 180 none 2.2(1)×10 −6 T93 27 GEP 4 20 - 0.625 µM 300 300 10 s, pH 1.5 None detected T93 75 GEP 6 1 µM 120 180 none None detected T93 75 GEP 7 25 - 0.098 µM 120 180 none 5.23(6)×10 −6 T93 27 GEP 8 20 - 0.156 µM 120 180 none 3.1(3)×10 −6 T344 28 4E10 10 - 0.625 nM 420 800 10 s, pH 1.5 1.08(1)×10 6 3.67(1)×10 −4 3.41(1)×10 −10 T344 28 GEP 1 43 - 0.084 µM 120 180 none 6.4(6)×10 −6 T344 28 GEP 2 50 - 0.098 µM 120 180 none 8(1)×10 −6 T344 35 GEP 3 20 - 0.156 µM 120 180 none 4.8(3)×10 −6 T344 35 GEP 4 20 - 0.625 µM 300 300 10 s, pH 1.5 None detected T344 35 GEP 7 20 - 0.156 µM 120 180 none 5.7(4)×10 −6 T344 35 GEP 8 20 - 0.156 µM 120 180 none 5.2(4)×10 −6 4E10- and GEP-ES complex structures show binding site conservation In order to shed light on potential structural differences accounting for reduced GEP binding affinities, crystal structures of GEP 1, 2 and 7 in complex with T117 were determined at resolution values of 2.9 Å, 1.8 Å, and 3.1 Å respectively, rebuilt and refined with good statistics ( Table 2 ), and compared to two reference 4E10/antigen complex structures: 4E10 bound to an epitope peptide (2FX7.

4E10 and GEP residues are shown in licorice stick representation and colored as follows: 4E10 Fv (3LH2.

HCDR flexibility is highlighted by F29H, which is able to flip out into solvent in the unbound 4E10 and GEP 1 structures, allowing HCDR1 to dynamically sample multiple conformers.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4304871

The complexes of 4E10 Fab with SAH-MPER (671-683KKK) (q) and the original (unmodified) 4E10-epitope peptide (PDB 2FX7) 18 superimpose with a root-mean-square-deviation of 0.73 Å for the C�... b1; atoms, and are overall very similar ( Supplementary Fig. 1b ).

However, the final 2Fo-Fc density at the Dab level ( Supplementary Fig. 4b ) improved after refinement compared with the density for the SAH-MPER (671-683KKK) (q) K683 ( Fig. 4b ) or with the density for the same lysine in the 1.76 Å structure of native MPER (671-683KKK) in complex with 4E10 (PDB entry 2FX7) 18 , where density was observed only for the main chain.

ACCESSION CODES The atomic coordinates and structure factors of the 4E10 Fab–SAH-MPER (671-683KKK) (q), 4E10 Fab–SAH-MPER (671-683KKK) (q)pSer, and 10E8 Fab–SAH-MPER (662-683KKK) (B,q) complexes have been deposited in the Protein Data Bank, with the accession codes 4NHC, 4NGH and 4U6G, respectively.

The superimposition of the phosphate-incorporated site with the same region in the 4E10 Fab–native MPER (671-683KKK) complex (PDB entry 2FX7) 18 , which was crystallized from phosphate-free buffer, demonstrates torqueing of backbone amides and reorientation of the S28 (H) hydroxyl toward the phosphate ion to promote favorable hydrogen bond interactions in the 4E10 Fab–SAH-MPER (671-683KKK) (q) structure ( Fig. 4c ).

(c) Superimposition of the phosphate-incorporated site of the 4E10 Fab–SAH-MPER (671-683KKK) (q) structure (gray) with that region of the 4E10 Fab–native MPER (671-683KKK) peptide complex (green; PDB entry 2FX7 18 ).

To our knowledge, we have detected this phosphate-binding site in the 4E10 combining region for the first time, as a PDB search of all available 4E10 structures did not reveal phosphate as a buffer component of prior crystallization conditions.

A recent crystal structure of the 4E10 variable region (Fv) in an unliganded form 49 shows sulfate ions near the CDR-H1 loop, but none of the ions are in the same position as observed here for the phosphate.

(b) Crystal structure of the SAH-MPER (671-683KKK) (q)pSer complex (shown as a green ribbon and wheat transparent Van der Waals surface) bound to 4E10 at 2.68 Å resolution.

Whereas sulfate and phosphate ions are similar, and can occupy the same binding site in a protein, the peptide-free structure of 4E10 49 has its CDR-H1 and CDR-H3 loops drastically perturbed compared to the peptide-bound form 18 .

Fmoc, Fluorenylmethoxycarbonyl Figure 3 Structural Analysis of the 4E10 Fab–SAH-MPER (671-683KKK) (q) Complex (a) Crystal structure of SAH-MPER (671-683KKK) (q) (shown as a blue ribbon and gray transparent van der Waals surface) bound to 4E10 Fab at 2.9 Å resolution.

The 4E10 Fab complexes with SAH-MPER (671-683KKK) (q)pSer and SAH-MPER (671-683KKK) (q) are otherwise very similar with only 0.23 Å r.m.s. deviation (all Cα atoms) for the Fab and 0.17 Å r.m.s. deviation (all Cα atoms) for the corresponding peptides ( Supplementary Fig. 1b and Supplementary Fig. 3c ).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4369679

Methodology Sequence Analysis : FASTA format of six amino acid sequences, three chains of two trimers, HIV-1 envelope glycoproteins i.e., 2M7W and 2LP7 from PDB containing the target for 4E10, 10E8 an... Z13 antibodies were downloaded.

Publication Year: 2015