9cqc

The ligation complex like in the NHEJ pathway

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

X-ray repair cross-complementing protein 6

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 5 × 2 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 4 （Q13426） DNA ligase 4 × 2 （P49917） Protein PAXX × 2 （Q9BUH6） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–612； UniProt 1–609 Author chain a； PDBConstruct 4–612； UniProt 1–609

X-ray repair cross-complementing protein 5

Homo sapiens

UniProt P13010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 6 × 2 （P12956） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 4 （Q13426） DNA ligase 4 × 2 （P49917） Protein PAXX × 2 （Q9BUH6） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–732； UniProt 1–732 Author chain b； PDBConstruct 1–732； UniProt 1–732

Non-homologous end-joining factor 1

Homo sapiens

UniProt Q9H9Q4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） DNA repair protein XRCC4 × 4 （Q13426） DNA ligase 4 × 2 （P49917） Protein PAXX × 2 （Q9BUH6） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHEJ1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–302； UniProt 1–299 Author chain c； PDBConstruct 4–302； UniProt 1–299

DNA repair protein XRCC4

Homo sapiens

UniProt Q13426

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA ligase 4 × 2 （P49917） Protein PAXX × 2 （Q9BUH6） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–336； UniProt 1–336 Author chain E； PDBConstruct 1–336； UniProt 1–336 Author chain d； PDBConstruct 1–336； UniProt 1–336 Author chain e； PDBConstruct 1–336； UniProt 1–336

DNA ligase 4

Homo sapiens

UniProt P49917

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 4 （Q13426） Protein PAXX × 2 （Q9BUH6） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNLI4_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 4–914； UniProt 1–911 Author chain f； PDBConstruct 4–914； UniProt 1–911

Protein PAXX

Homo sapiens

UniProt Q9BUH6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 14 DNA 4	X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 4 （Q13426） DNA ligase 4 × 2 （P49917） DNA (38-MER) × 1 DNA (40-MER) × 1 DNA (34-MER) × 1 DNA (35-MER) × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAXX_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 15–218； UniProt 1–204 Author chain H； PDBConstruct 15–218； UniProt 1–204

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9cqc
Deposition date deposition_date	2024-07-19
Structure title title	The ligation complex like in the NHEJ pathway
Keywords keywords	NHEJ, ligation, XLF, PAXX, DNA repair, Ligase IV, LIGASE-TRANSFERASE-DNA complex; LIGASE/TRANSFERASE/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9cqc__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9cqc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cqc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	77.21 Å
Rg (electron density)	77.48 Å
Total Rg	77.25 Å
Atom count	39138
Residues	4639
Excluded volume	690760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cqc__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	X-ray repair cross-complementing protein 6
Molecular weight formula_weight	70198.3 kDa
EC 编号 ec_number	3.6.4.-,4.2.99.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a
Atom count atom_count	39149

GPVMSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	X-ray repair cross-complementing protein 5
Molecular weight formula_weight	82812.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b

MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFEEGGDVDDLLDMI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Non-homologous end-joining factor 1
Molecular weight formula_weight	33625.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,c

GPVMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGDPHTSNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGLFS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	DNA repair protein XRCC4
Molecular weight formula_weight	38337.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,d,e

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSRPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDEI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	DNA ligase 4
Molecular weight formula_weight	104378.2 kDa
EC 编号 ec_number	6.5.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,f

GPVMAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHGDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDISITLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSILCGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMTLDDLEQLRGKASGKLASKHLYIGGDDEPQEKKRKAAPKMKKVIGIIEHLKAPNLTNVNKISNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGPDTYCVIAGSENIRVKNIILSNKHDVVKPAWLLECFKTKSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSMFRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRRTFKRKFKILKESWVTDSIDKCELQEENQYLI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Protein PAXX
Molecular weight formula_weight	23282.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MGSSHHHHHHSQDPMDPLSPPLCTLPPGPEPPRFVCYCEGEESGEGDRGGFNLYVTDAAELWSTCFTPDSLAALKARFGLSAAEDITPRFRAACEQQAVALTLQEDRASLTLSGGPSALAFDLSKVPGPEAAPRLRALTLGLAKRVWSLERRLAAAEETAVSPRKSPRPAGPQLFLPDPDPQRGGPGPGVRRRCPGESLINPGFKSKKPAGGVDFDET

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	DNA (38-MER)
Molecular weight formula_weight	20737.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAACTATGCATGCTCTACTGCTTCTGATCTAGTCGACT

Entity 8 Entity 8 polymer

Description description	DNA (40-MER)
Molecular weight formula_weight	20795.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAACATTCGTTCACGTGAGTTCCAGTACAAGTCTAGTC

Entity 9 Entity 9 polymer

Description description	DNA (34-MER)
Molecular weight formula_weight	15865.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

GACTAGATCAGAAGCAGTAGAGCATGCATAGTTTTTAGTTTATTGGGCGCG

Entity 10 Entity 10 polymer

Description description	DNA (35-MER)
Molecular weight formula_weight	15493.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

GACTTGTACTGGAACTCACGTGAACGAATGTTTTTAGTTTATTGGGCGCG

Entity 11 Entity 11 non-polymer

Description description	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
Molecular weight formula_weight	490.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	133163

The ligation complex like in the NHEJ pathway

1. Protein Identity and Related Structures Protein Identity & Related Structures

X-ray repair cross-complementing protein 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

X-ray repair cross-complementing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Non-homologous end-joining factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA repair protein XRCC4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA ligase 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein PAXX

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cqc__assembly_1__model_1

9cqc__assembly_1__model_1 | I(q)

9cqc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer